Data collection and phylogeny

Toxin expression data were collected from 39 publications (Supplementary table 1). The selection criteria for toxins and taxa are the same as in (Barua and Mikheyev 2019). We scaled gene expression levels by the average within-species variance allowing us to standardize the measurements and carry out comparisons across toxins. This scaled dataset was used in all subsequent analysis. We used a previously described time-calibrated phylogeny of squamates based on two large datasets comprising of 44 nuclear genes for 161 squamates, and a dataset of 12 genes from 4161 squamate species, both these datasets represented families and subfamilies (Wiens et al. 2012; Pyron et al. 2013; Zheng and Wiens 2016; Barua and Mikheyev 2019).

library(tidyverse)
library(ggplot2)
library(reshape2)
library(geiger)
library(spptest)
library(BAMMtools)
library(ape)
library(phytools)
library(coda)
library(kableExtra)
library(OUwie)

Check tree

tree <- read.newick("./Final_tree.tre")
plotTree(tree)

Check if tree is ultrametric

is.ultrametric(tree)
## [1] TRUE


Load data

Toxin expression data was collected from 39 publications (online supp). Out of the 25 reported toxin families we selected only 10 as they were the most ubiquitous toxins amongst all snakes. We restricted our dataset to include components that are found in at least 50% of snakes and eliminated low-abundance toxin families (Supplementary Fig 34 & 35). Incidentally, this cutoff also eliminated many low-abundance toxin families (on average less than 1% of the venom). The abundance of these toxins would be more difficult to estimate, as they are closer to the signal to noise to threshold of gene expression experiments. Overall 10 out of 25 toxin families we retained. Toxins levels were recorded as per publication. Toxin values reported as absolute FPKM values, were converted to a percentages of total toxin transcript expression.

dat<-read.csv("./data/scaleddata/vPhen_data.csv", header = T)

Supplementary Table 1: Gene expression values and references

species TFTx BPP.CNP CRISP CTL GF KSPI LAAO ePLA2 vPLA2 SVMP SVSP Total cm Family Author Tech Ref
Agkistrodon_piscivorus 0.00000 0.04570 0.00000 0.06080 0.00000 0.00000 0.00000 0.00000 0.38960 0.34900 0.08300 0.92810 127.0 Viperidae Aronow (2018) Illumina https://search.proquest.com/openview/2997dede40d17e51e7dabfd03d9762df/1?pq-origsite=gscholar&cbl=18750&diss=y
Atropoides_picadoi 0.00400 0.16400 0.02600 0.04800 0.00600 0.00010 0.03100 0.00000 0.02300 0.56100 0.10900 0.97210 120.2 Viperidae Durban et al. (2011) Roche GS FLX https://doi.org/10.1186/1471-2164-12-259
Bitis_gabonica 0.00000 0.01813 0.00000 0.07591 0.03626 0.09064 0.05665 0.00000 0.05665 0.37729 0.14729 0.85882 120.0 Viperidae Francischetti et al. (2004) Beckman Coulter https://doi.org/10.1016/j.gene.2004.03.024
Boiga_irregularis 0.67475 0.01400 0.03835 0.02271 0.00025 0.00100 0.00000 0.00040 0.00000 0.24854 0.00000 1.00000 270.0 Colubridae McGivern et al. (2014) Illumina https://doi.org/10.1186/1471-2164-15-1061
Bothriechis_lateralis 0.01600 0.23600 0.03200 0.03100 0.01800 0.00020 0.03400 0.00000 0.03000 0.44900 0.10400 0.95020 90.0 Viperidae Durban et al. (2011) Roche GS FLX https://doi.org/10.1186/1471-2164-12-259
Bothriechis_schlegelii 0.03600 0.15300 0.03600 0.00200 0.04900 0.00120 0.03200 0.00000 0.09200 0.26300 0.20500 0.86920 55.0 Viperidae Durban et al. (2011) Roche GS FLX https://doi.org/10.1186/1471-2164-12-259
Bothrops_alternatus 0.00000 0.11800 0.02200 0.16500 0.02500 0.00000 0.01800 0.00000 0.01400 0.58500 0.05100 0.99800 100.0 Viperidae Pereira de Paula et al. (2014) MegaBACE (GE) https://doi.org/10.1016/j.cbd.2014.09.001
Bothrops_asper 0.00800 0.15000 0.00800 0.01000 0.00000 0.00030 0.04200 0.00000 0.17800 0.41600 0.13400 0.94630 150.0 Viperidae Durban et al. (2011) Roche GS FLX https://doi.org/10.1186/1471-2164-12-259
Bothrops_atrox 0.00000 0.07100 0.00500 0.04800 0.01000 0.00000 0.01400 0.00000 0.14600 0.61600 0.08200 0.99200 100.0 Viperidae Neiva et al. (2009) MegaBACE (GE) https://doi.org/10.1016/j.toxicon.2009.01.006
Bothrops_colombiensis 0.00000 0.01000 0.02000 0.04000 0.02000 0.00000 0.02000 0.00000 0.30000 0.37000 0.12000 0.90000 100.0 Viperidae Suntravat et al. (2016) ABI 3730 https://doi.org/10.1186/s12867-016-0059-7
Bothrops_insularis 0.00000 0.15800 0.01500 0.14200 0.05100 0.00000 0.03500 0.00000 0.05400 0.43200 0.11200 0.99900 150.0 Viperidae Valente et al. (2009) ABI 3100 https://doi.org/10.1016/j.jprot.2009.01.001
Bothrops_jararaca 0.00000 0.04250 0.00400 0.13650 0.02900 0.00200 0.04050 0.00000 0.03600 0.43600 0.26100 0.98750 160.0 Viperidae Goncalves-Machado et al. (2016) Roche GS FLX https://doi.org/10.1016/j.jprot.2015.04.029
Bothrops_jararacussu 0.00000 0.01695 0.03390 0.08475 0.00000 0.00000 0.01695 0.00000 0.56290 0.25820 0.01695 0.99060 70.0 Viperidae Kashima et al. (2004) ABI 3100 https://doi.org/10.1016/j.biochi.2004.02.002
Bothrops_moojeni 0.00060 0.00950 0.00570 0.02670 0.00000 0.00440 0.01270 0.00000 0.09020 0.46630 0.26180 0.87790 130.0 Viperidae Amorim et al. (2017) Illumina https://doi.org/10.1016/j.toxicon.2017.10.025
Bothrops_neuwiedi 0.00000 0.17400 0.00700 0.08600 0.00360 0.00000 0.02900 0.00000 0.26400 0.36000 0.05300 0.97660 65.0 Viperidae Rodigues et al. (2012) MegaBACE (GE) https://doi.org/10.1016/j.jprot.2012.03.028
Bungarus_flaviceps 0.39290 0.00000 0.00440 0.00440 0.00000 0.24060 0.00000 0.35320 0.00000 0.00000 0.00000 0.99550 185.0 Elapidae Siang et al. (2010) ABI PRISM https://dx.doi.org/10.1186/1471-2199-11-24
Bungarus_multicinctus 0.64700 0.00000 0.00700 0.03800 0.00200 0.10600 0.00100 0.17400 0.00000 0.00000 0.00100 0.97600 125.0 Elapidae Jiang et al. (2011) ABI 3100 https://doi.org/10.1186/1471-2164-12-1
Cerrophidion_godmani 0.00600 0.08300 0.02600 0.00200 0.00600 0.00000 0.05500 0.00000 0.07900 0.42200 0.28100 0.96000 55.0 Viperidae Durban et al. (2011) Roche GS FLX https://doi.org/10.1186/1471-2164-12-259
Crotalus_adamanteus 0.00000 0.00726 0.01317 0.22155 0.00023 0.00054 0.05309 0.00000 0.07810 0.24410 0.19979 0.81783 244.0 Viperidae Rokyta et al. (2012) Illumina https://doi.org/10.1186/1471-2164-13-312
Crotalus_durissus 0.00000 0.00000 0.00000 0.00000 0.04000 0.00000 0.00000 0.00000 0.88000 0.03000 0.02500 0.97500 150.0 Viperidae Boldrini-Franca et al. (2009) MegaBACE (GE) https://doi.org/10.1016/j.biochi.2009.02.001
Crotalus_horridus 0.00000 0.12519 0.00775 0.00213 0.02285 0.00119 0.01106 0.00000 0.22772 0.00111 0.58229 0.98129 121.0 Viperidae Rokyta et al. (2013) Illumina https://doi.org/10.1186/1471-2164-14-394
Crotalus_scutulatus 0.00000 0.20121 0.00481 0.16943 0.02000 0.00021 0.00925 0.00000 0.18171 0.14363 0.11692 0.84717 137.3 Viperidae Strickland et al. (2018) Illumina https://dx.doi.org/10.3390/toxins10040135
Crotalus_simus 0.12700 0.13400 0.00000 0.02400 0.00000 0.00150 0.03800 0.00000 0.12100 0.06500 0.28100 0.79150 150.0 Viperidae Durban et al. (2011) Roche GS FLX https://doi.org/10.1186/1471-2164-12-259
Dispholidus_typus 0.06200 0.00000 0.05400 0.00400 0.00100 0.00150 0.00000 0.07600 0.00000 0.74640 0.05500 0.99990 135.0 Colubridae Pla et al. (2017) Illumina https://doi.org/10.1016/j.bbagen.2017.01.020
Drysdalia_coronoides 0.86000 0.00000 0.02800 0.00000 0.01400 0.00000 0.00000 0.00240 0.00000 0.00000 0.09200 0.99640 40.0 Elapidae Chatrath et al. (2011) ABI PRISM https://dx.doi.org/10.1021/pr1008916
Echis_carinatus 0.00000 0.00000 0.01934 0.17602 0.00580 0.00193 0.01161 0.00000 0.08317 0.64603 0.04836 0.99226 60.0 Viperidae Casewell et al. (2009) ABI 3730 https://doi.org/10.1186/1471-2164-10-564
Echis_coloratus 0.00000 0.00000 0.05426 0.10543 0.00620 0.00000 0.04031 0.00000 0.05426 0.68527 0.04496 0.99069 62.7 Viperidae Casewell et al. (2009) ABI 3730 https://doi.org/10.1186/1471-2164-10-564
Echis_ocellatus 0.00000 0.00000 0.00297 0.10979 0.02671 0.00193 0.01187 0.00000 0.08605 0.73591 0.02374 0.99897 40.0 Viperidae Casewell et al. (2009) ABI 3730 https://doi.org/10.1186/1471-2164-10-564
Echis_pyramidum 0.00000 0.00000 0.00000 0.24011 0.00582 0.00000 0.02639 0.00000 0.20580 0.50000 0.01979 0.99791 65.0 Viperidae Casewell et al. (2009) ABI 3730 https://doi.org/10.1186/1471-2164-10-564
Gloydius_intermedius 0.00000 0.04900 0.04900 0.04900 0.14600 0.00000 0.02400 0.00000 0.12200 0.17000 0.22000 0.82900 53.3 Viperidae Yang et al. (2015) MegaBACE (GE) https://doi.org/10.1016/j.toxicon.2015.08.010
Hypsiglena_torquata 0.00070 0.07359 0.16684 0.06176 0.00012 0.00056 0.00000 0.00000 0.00000 0.68666 0.00000 0.99023 48.0 Colubridae McGivern et al. (2014) Illumina https://doi.org/10.1186/1471-2164-15-1061
Lachesis_muta 0.01600 0.73200 0.00000 0.05800 0.00300 0.00000 0.03700 0.00000 0.04700 0.05900 0.03500 0.98700 225.0 Viperidae Lnacio et al. (2007) ABI 3100 https://doi.org/10.1534/genetics.106.056515
Micrurus_altirostris 0.86400 0.00000 0.00000 0.01300 0.00000 0.03800 0.00000 0.04900 0.00000 0.00600 0.00000 0.97000 64.0 Elapidae Correa-Netto et al. (2011) ABI 3100 https://doi.org/10.1016/j.jprot.2011.04.003
Micrurus_corallinus 0.20300 0.29530 0.00000 0.06700 0.01830 0.00150 0.00840 0.37680 0.00000 0.02100 0.00100 0.99230 72.5 Elapidae Aird et al. (2017) Illumina https://dx.doi.org/10.3390/toxins9060187
Micrurus_fulvius 0.25160 0.00000 0.00000 0.00799 0.01600 0.02154 0.00880 0.64947 0.00000 0.02947 0.00000 0.98487 55.0 Elapidae Margres et al. (2013) Illumina https://doi.org/10.1186/1471-2164-14-531
Micrurus_lemniscatus 0.67220 0.00200 0.00240 0.00480 0.01420 0.07150 0.00730 0.17200 0.00000 0.01120 0.00100 0.95860 120.0 Elapidae Aird et al. (2017) Illumina https://dx.doi.org/10.3390/toxins9060187
Micrurus_spixii 0.62640 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.36390 0.00000 0.00000 0.00000 0.99030 75.0 Elapidae Aird et al. (2017) Illumina https://dx.doi.org/10.3390/toxins9060187
Micrurus_surinamensis 0.60240 0.02670 0.00000 0.00340 0.07880 0.01070 0.00000 0.26230 0.00000 0.00140 0.00000 0.98570 68.0 Elapidae Aird et al. (2017) Illumina https://dx.doi.org/10.3390/toxins9060187
Naja_atra 0.95800 0.00000 0.00700 0.00600 0.00100 0.00100 0.00100 0.01200 0.00000 0.00400 0.00000 0.99000 150.0 Elapidae Jiang et al. (2011) ABI 3100 https://doi.org/10.1186/1471-2164-12-1
Naja_kaouthia 0.82000 0.00000 0.00000 0.00500 0.00300 0.00100 0.00200 0.13600 0.00000 0.01100 0.00000 0.97800 150.0 Elapidae Xu et al. (2017) Illumina https://doi.org/10.1016/j.jprot.2017.02.018
Opheodrys_aestivus 0.13300 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.03600 0.00000 0.00000 0.00000 0.16900 91.5 Colubridae Hargreaves et al. (2014) Illumina https://doi.org/10.1016/j.toxicon.2014.10.004
Ophiophagus_hannah 0.43000 0.00000 0.08700 0.00000 0.00800 0.01000 0.05700 0.04000 0.00000 0.24400 0.00700 0.88300 425.0 Elapidae Tan et al. (2015) Illumina https://dx.doi.org/10.1186/s12864-015-1828-2
Ovophis_okinavensis 0.00000 0.00000 0.00000 0.00579 0.00008 0.00000 0.00623 0.00000 0.00647 0.04220 0.86176 0.92253 55.0 Viperidae Aird et al. (2013) Illumina https://doi.org/10.1186/1471-2164-14-790
Pantherophis_guttatus 0.01000 0.00000 0.02200 0.00000 0.00000 0.00000 0.00000 0.12900 0.00000 0.00000 0.00000 0.16100 150.0 Colubridae Hargreaves et al. (2014) Illumina https://doi.org/10.1016/j.toxicon.2014.10.004
Phalotris_mertensi 0.01800 0.00140 0.00330 0.21600 0.00040 0.43900 0.02300 0.00000 0.00000 0.22040 0.00220 0.92370 100.0 Colubridae Campos et al. (2016) ABI 3100 https://doi.org/10.1093/gbe/evw149
Philodryas_olfersii 0.00000 0.22400 0.10400 0.05800 0.00000 0.00000 0.00000 0.00000 0.00000 0.52400 0.08900 0.99900 125.0 Colubridae Ching et al. (2006) ABI 3100 https://doi.org/10.1016/j.febslet.2006.07.010
Protobothrops_elegans 0.00000 0.01400 0.00001 0.00200 0.00600 0.00000 0.00500 0.00000 0.77100 0.08100 0.10400 0.98301 120.0 Viperidae Aird et al. (2015) Illumina https://doi.org/10.1186/s12864-015-1832-6
Protobothrops_flavoviridis 0.00000 0.00000 0.03854 0.15356 0.00960 0.00000 0.09071 0.00000 0.32136 0.26975 0.11054 0.99406 137.0 Viperidae Aird et al. (2013) Illumina https://doi.org/10.1186/1471-2164-14-790
Protobothrops_mucrosquamatus 0.00000 0.00000 0.01018 0.01018 0.00647 0.00000 0.01200 0.00000 0.25746 0.39966 0.28076 0.97671 116.0 Viperidae Aird et al. (2017) Illumina https://doi.org/10.1093/gbe/evx199
Pseudonaja_textilis 0.10633 0.00000 0.03846 0.00000 0.00452 0.01810 0.00000 0.18778 0.00000 0.00000 0.42534 0.78053 150.0 Elapidae Reeks et al. (2016) Roche GS FLX https://doi.org/10.1016/j.jprot.2015.11.019
Sistrurus_catenatus 0.00830 0.00280 0.06670 0.01390 0.06670 0.00000 0.03610 0.00000 0.28060 0.12220 0.37500 0.97230 73.5 Viperidae Pahari et al. (2007) ABI 3100 https://doi.org/10.1186/1471-2199-8-115
Thamnodynastes_strigatus 0.00200 0.00000 0.01900 0.05400 0.00000 0.00000 0.00000 0.00000 0.00000 0.84400 0.00700 0.92600 70.0 Colubridae Ching et al. (2011) ABI 3100 https://dx.doi.org/10.1021/pr200876c


Scaled version of this dataset was used in all subsequent analysis

#normalize data
scaled.dat <- dat
scaled.dat[,2:12] <- t(scale(t(scaled.dat[,2:12])))

Removing low abundance toxins.

all_dat<-read.csv("./data/scaleddata/All_25_comps.csv", header = T)

Supplementary Figure 1: Average compositon of each toxin in the venom of 52 species in our study

Supplementary Figure 2: Tiles plot showing presence/absensce of each toxin in 52 snake species

Coloured tiles indicate presence of toxin, while white tiles indicate absence. As oberserved from the plot we included components that are found in at least 50% of snakes (Red dashed line). This ensured low retention of structural zeros in our complete dataset.

DTT Analysis

Higher between clade disparity in phenotypes (disparity between large diversifying lineages) is an indicator of ‘early burst’ evolution (Simpson 1953.; Tran Lucy A. P. 2014). Disparity through time measures instances when disparity was highest within versus among subclades (Harmon et al. 2003; Tran Lucy A. P. 2014). It also provides us an estimate of whether phenotypic diversity occurred early or late in the diversification process. We performed a disparity through time (DTT) analysis to get estimates of when overall disparity in toxin levels arose and the subsequent trends they experienced.

Load data

tree<-read.newick("./Final_tree.tre")
trait<-read.csv("./data/scaleddata/scaled_data_fot_dtt.csv",row.names = 1, header = T)

BPP

The following script was repeated for all 11 toxins

trait<-as.matrix(trait)[,'BPP.CNP']
venomdtt <-dtt(tree, trait, index = 'avg.sq', nsim = 5000,
               CI = 0.95, plot = F)

Rank envelope function taken from (Murrell 2018)

rank_env_dtt(venomdtt)

## Rank envelope test
##  p-value of the test: 0.00379924 (ties method: midrank)
##  p-interval         : (0.00019996, 0.00739852)



CRISP

## Rank envelope test
##  p-value of the test: 0.00389922 (ties method: midrank)
##  p-interval         : (0.00019996, 0.00759848)



CTL

## Rank envelope test
##  p-value of the test: 0.03719256 (ties method: midrank)
##  p-interval         : (0.03479304, 0.03959208)

GF

## Rank envelope test
##  p-value of the test: 0.00379924 (ties method: midrank)
##  p-interval         : (0.00019996, 0.00739852)



KSPI

## Rank envelope test
##  p-value of the test: 0.00459908 (ties method: midrank)
##  p-interval         : (0.00019996, 0.0089982)



LAAO

## Rank envelope test
##  p-value of the test: 0.00379924 (ties method: midrank)
##  p-interval         : (0.00019996, 0.00739852)



SVMP

## Rank envelope test
##  p-value of the test: 0.3285343 (ties method: midrank)
##  p-interval         : (0.3273345, 0.3297341)



SVSP

## Rank envelope test
##  p-value of the test: 0.00429914 (ties method: midrank)
##  p-interval         : (0.00019996, 0.00839832)



TFTx

## Rank envelope test
##  p-value of the test: 0.01209758 (ties method: midrank)
##  p-interval         : (0.00839832, 0.01579684)



vPLA2

## Rank envelope test
##  p-value of the test: 0.00429914 (ties method: midrank)
##  p-interval         : (0.00019996, 0.00839832)



ePLA2

## Rank envelope test
##  p-value of the test: 0.2178564 (ties method: midrank)
##  p-interval         : (0.2159568, 0.219756)

Bayesian analysis of macroevolutionary mixtures (BAMM)

We estimated evolutionary rate dynamics under the Bayesian analysis of macroevolutionary mixtures (BAMM), to observe shifts in rates of gene expression evolution that took place at different points throughout the history of snake venom evolution. Parameters for phenotypic evolution suggested in the online BAMM documentation (http://bamm-project.org/) were used to run the model. The model was run for 108 generations with MCMC write frequency of 104. Priors were obtained using the setBAMMpriors function in BAMMTools (Rabosky et al. 2014).

Supplementary Figure 3: Convergence diagnosis of MCMC chiains

Convergence of MCMC chains were determined by visual inspection, and plotting effective sample size of log-likelihood and number of shifts in each sample, both of which well exceeded the recommended value of 200

BPP

mcmcout<- read.csv("./Analysis_scaled/ControlFiles_scaleddata/BPP/mcmc_out.txt", header = T)
plot(mcmcout$logLik ~ mcmcout$generation, type="l")

burnstart <- floor(0.8 * nrow(mcmcout))
postburn <- mcmcout[burnstart:nrow(mcmcout),]

effectiveSize(postburn$N_shifts)
##     var1 
## 1873.928
effectiveSize(postburn$logLik)
##     var1 
## 1743.364
plot(postburn$logLik ~ postburn$generation, type="l")

plotPrior(mcmcout, expectedNumberOfShifts = 1)



CRISP

## var1 
## 8001
##     var1 
## 6696.861



CTL

##     var1 
## 7961.472
## var1 
## 9001



GF

## var1 
## 9001
##     var1 
## 8567.747



KUN

##     var1 
## 6775.222
##     var1 
## 5244.185



LAAO

## var1 
## 3001
## var1 
## 3001



ePLA2

##    var1 
## 2353.79
##     var1 
## 1715.655



vPLA2

##     var1 
## 1750.436
##     var1 
## 1777.745



SVMP

##     var1 
## 8014.687
##     var1 
## 7752.112



SVSP

## var1 
## 8501
##     var1 
## 7195.953



TFTx

##     var1 
## 3196.441
##    var1 
## 739.902

Computing Bayes factor

Bayes factor estimates support the occurrence of at least one rate shift in all toxin families, indicating that toxins families have experienced changes in their evolutionary rates since becoming a part of the venom arsenal. A Bayes factor of 20 and above means that we have enough certainty that the number of rate shifts above the lowest number of shifts in likely.

Supplementary Figure 4: Bayes factor estimates for shift configurations

BPP

mcmcout<- read.csv("./Analysis_scaled/ControlFiles_scaleddata/BPP/mcmc_out.txt", header = T)

bfmat<-computeBayesFactors(mcmcout,expectedNumberOfShifts = 1, burnin = 0.8)

# Bayes factor matrix
bfmat
##            3         4         5         6         7         8         9
## 3   1.000000 0.3031136 0.1872172 0.1277006 0.1004248 0.1136676 0.1261433
## 4   3.299094 1.0000000 0.6176471 0.4212963 0.3313107 0.3750000 0.4161585
## 5   5.341390 1.6190476 1.0000000 0.6820988 0.5364078 0.6071429 0.6737805
## 6   7.830816 2.3736264 1.4660633 1.0000000 0.7864078 0.8901099 0.9878049
## 7   9.957704 3.0183150 1.8642534 1.2716049 1.0000000 1.1318681 1.2560976
## 8   8.797583 2.6666667 1.6470588 1.1234568 0.8834951 1.0000000 1.1097561
## 9   7.927492 2.4029304 1.4841629 1.0123457 0.7961165 0.9010989 1.0000000
## 10  4.640483 1.4065934 0.8687783 0.5925926 0.4660194 0.5274725 0.5853659
## 11  3.093656 0.9377289 0.5791855 0.3950617 0.3106796 0.3516484 0.3902439
## 12  3.093656 0.9377289 0.5791855 0.3950617 0.3106796 0.3516484 0.3902439
## 14  6.187311 1.8754579 1.1583710 0.7901235 0.6213592 0.7032967 0.7804878
## 15 12.374622 3.7509158 2.3167421 1.5802469 1.2427184 1.4065934 1.5609756
##           10        11        12        14         15
## 3  0.2154948 0.3232422 0.3232422 0.1616211 0.08081055
## 4  0.7109375 1.0664062 1.0664063 0.5332031 0.26660156
## 5  1.1510417 1.7265625 1.7265625 0.8632813 0.43164063
## 6  1.6875000 2.5312500 2.5312500 1.2656250 0.63281250
## 7  2.1458333 3.2187500 3.2187500 1.6093750 0.80468750
## 8  1.8958333 2.8437500 2.8437500 1.4218750 0.71093750
## 9  1.7083333 2.5625000 2.5625000 1.2812500 0.64062500
## 10 1.0000000 1.5000000 1.5000000 0.7500000 0.37500000
## 11 0.6666667 1.0000000 1.0000000 0.5000000 0.25000000
## 12 0.6666667 1.0000000 1.0000000 0.5000000 0.25000000
## 14 1.3333333 2.0000000 2.0000000 1.0000000 0.50000000
## 15 2.6666667 4.0000000 4.0000000 2.0000000 1.00000000

CRISP

##            0           1           2            3            4           5
## 0     1.0000 0.002663116 0.001402525 0.0009784736 0.0008116883 0.000697026
## 1   375.5000 1.000000000 0.526647966 0.3674168297 0.3047889610 0.261733271
## 2   713.0000 1.898801598 1.000000000 0.6976516634 0.5787337662 0.496979554
## 3  1022.0000 2.721704394 1.433380084 1.0000000000 0.8295454545 0.712360595
## 4  1232.0000 3.280958722 1.727910238 1.2054794521 1.0000000000 0.858736059
## 5  1434.6667 3.820683533 2.012155213 1.4037834312 1.1645021645 1.000000000
## 6  1562.6667 4.161562361 2.191678354 1.5290280496 1.2683982684 1.089219331
## 7  1664.0000 4.431424767 2.333800842 1.6281800391 1.3506493506 1.159851301
## 8  1664.0000 4.431424767 2.333800842 1.6281800391 1.3506493506 1.159851301
## 9  1877.3333 4.999556147 2.633006078 1.8369210698 1.5238095238 1.308550186
## 10 1450.6667 3.863293387 2.034595605 1.4194390085 1.1774891775 1.011152416
## 11 1536.0000 4.090545939 2.154277700 1.5029354207 1.2467532468 1.070631970
## 12 1024.0000 2.727030626 1.436185133 1.0019569472 0.8311688312 0.713754647
## 13  682.6667 1.818020417 0.957456755 0.6679712981 0.5541125541 0.475836431
## 14 1365.3333 3.636040834 1.914913511 1.3359425962 1.1082251082 0.951672862
##               6            7            8            9           10
## 0  0.0006399317 0.0006009615 0.0006009615 0.0005326705 0.0006893382
## 1  0.2402943686 0.2256610577 0.2256610577 0.2000177557 0.2588465074
## 2  0.4562713311 0.4284855769 0.4284855769 0.3797940341 0.4914981618
## 3  0.6540102389 0.6141826923 0.6141826923 0.5443892045 0.7045036765
## 4  0.7883959044 0.7403846154 0.7403846154 0.6562500000 0.8492647059
## 5  0.9180887372 0.8621794872 0.8621794872 0.7642045455 0.9889705882
## 6  1.0000000000 0.9391025641 0.9391025641 0.8323863636 1.0772058824
## 7  1.0648464164 1.0000000000 1.0000000000 0.8863636364 1.1470588235
## 8  1.0648464164 1.0000000000 1.0000000000 0.8863636364 1.1470588235
## 9  1.2013651877 1.1282051282 1.1282051282 1.0000000000 1.2941176471
## 10 0.9283276451 0.8717948718 0.8717948718 0.7727272727 1.0000000000
## 11 0.9829351536 0.9230769231 0.9230769231 0.8181818182 1.0588235294
## 12 0.6552901024 0.6153846154 0.6153846154 0.5454545455 0.7058823529
## 13 0.4368600683 0.4102564103 0.4102564103 0.3636363636 0.4705882353
## 14 0.8737201365 0.8205128205 0.8205128205 0.7272727273 0.9411764706
##              11           12          13           14
## 0  0.0006510417 0.0009765625 0.001464844 0.0007324219
## 1  0.2444661458 0.3666992188 0.550048828 0.2750244141
## 2  0.4641927083 0.6962890625 1.044433594 0.5222167969
## 3  0.6653645833 0.9980468750 1.497070313 0.7485351563
## 4  0.8020833333 1.2031250000 1.804687500 0.9023437500
## 5  0.9340277778 1.4010416667 2.101562500 1.0507812500
## 6  1.0173611111 1.5260416667 2.289062500 1.1445312500
## 7  1.0833333333 1.6250000000 2.437500000 1.2187500000
## 8  1.0833333333 1.6250000000 2.437500000 1.2187500000
## 9  1.2222222222 1.8333333333 2.750000000 1.3750000000
## 10 0.9444444444 1.4166666667 2.125000000 1.0625000000
## 11 1.0000000000 1.5000000000 2.250000000 1.1250000000
## 12 0.6666666667 1.0000000000 1.500000000 0.7500000000
## 13 0.4444444444 0.6666666667 1.000000000 0.5000000000
## 14 0.8888888889 1.3333333333 2.000000000 1.0000000000

CTL

##             1           2           3           4           5           6
## 1     1.00000  0.04133545 0.007011866 0.003128008 0.001852908 0.001314725
## 2    24.19231  1.00000000 0.169633225 0.075673725 0.044826112 0.031806230
## 3   142.61538  5.89507154 1.000000000 0.446102021 0.264253136 0.187500000
## 4   319.69231 13.21462639 2.241639698 1.000000000 0.592360319 0.420307443
## 5   539.69231 22.30842607 3.784250270 1.688161694 1.000000000 0.709546926
## 6   760.61538 31.44038156 5.333333333 2.379210780 1.409350057 1.000000000
## 7   836.92308 34.59459459 5.868392665 2.617901829 1.550741163 1.100323625
## 8   866.46154 35.81558029 6.075512406 2.710298364 1.605473204 1.139158576
## 9  1048.61538 43.34499205 7.352750809 3.280076997 1.942987457 1.378640777
## 10  836.92308 34.59459459 5.868392665 2.617901829 1.550741163 1.100323625
## 11  886.15385 36.62957075 6.213592233 2.771896054 1.641961231 1.165048544
## 12  512.00000 21.16375199 3.590075512 1.601539942 0.948688712 0.673139159
## 13  236.30769  9.76788553 1.656957929 0.739172281 0.437856328 0.310679612
## 14  472.61538 19.53577107 3.313915858 1.478344562 0.875712657 0.621359223
## 15  945.23077 39.07154213 6.627831715 2.956689124 1.751425314 1.242718447
## 16  630.15385 26.04769475 4.418554477 1.971126083 1.167616876 0.828478964
##              7           8            9          10          11
## 1  0.001194853 0.001154119 0.0009536385 0.001194853 0.001128472
## 2  0.028906250 0.027920810 0.0230707160 0.028906250 0.027300347
## 3  0.170404412 0.164595170 0.1360035211 0.170404412 0.160937500
## 4  0.381985294 0.368963068 0.3048708920 0.381985294 0.360763889
## 5  0.644852941 0.622869318 0.5146713615 0.644852941 0.609027778
## 6  0.908823529 0.877840909 0.7253521127 0.908823529 0.858333333
## 7  1.000000000 0.965909091 0.7981220657 1.000000000 0.944444444
## 8  1.035294118 1.000000000 0.8262910798 1.035294118 0.977777778
## 9  1.252941176 1.210227273 1.0000000000 1.252941176 1.183333333
## 10 1.000000000 0.965909091 0.7981220657 1.000000000 0.944444444
## 11 1.058823529 1.022727273 0.8450704225 1.058823529 1.000000000
## 12 0.611764706 0.590909091 0.4882629108 0.611764706 0.577777778
## 13 0.282352941 0.272727273 0.2253521127 0.282352941 0.266666667
## 14 0.564705882 0.545454545 0.4507042254 0.564705882 0.533333333
## 15 1.129411765 1.090909091 0.9014084507 1.129411765 1.066666667
## 16 0.752941176 0.727272727 0.6009389671 0.752941176 0.711111111
##             12          13          14          15          16
## 1  0.001953125 0.004231771 0.002115885 0.001057943 0.001586914
## 2  0.047250601 0.102376302 0.051188151 0.025594076 0.038391113
## 3  0.278545673 0.603515625 0.301757813 0.150878906 0.226318359
## 4  0.624399038 1.352864583 0.676432292 0.338216146 0.507324219
## 5  1.054086538 2.283854167 1.141927083 0.570963542 0.856445313
## 6  1.485576923 3.218750000 1.609375000 0.804687500 1.207031250
## 7  1.634615385 3.541666667 1.770833333 0.885416667 1.328125000
## 8  1.692307692 3.666666667 1.833333333 0.916666667 1.375000000
## 9  2.048076923 4.437500000 2.218750000 1.109375000 1.664062500
## 10 1.634615385 3.541666667 1.770833333 0.885416667 1.328125000
## 11 1.730769231 3.750000000 1.875000000 0.937500000 1.406250000
## 12 1.000000000 2.166666667 1.083333333 0.541666667 0.812500000
## 13 0.461538462 1.000000000 0.500000000 0.250000000 0.375000000
## 14 0.923076923 2.000000000 1.000000000 0.500000000 0.750000000
## 15 1.846153846 4.000000000 2.000000000 1.000000000 1.500000000
## 16 1.230769231 2.666666667 1.333333333 0.666666667 1.000000000

GF

##           1            2            3            4           5
## 1     1.000 0.0006912442 0.0003205128 0.0002042484 0.000161221
## 2  1446.667 1.0000000000 0.4636752137 0.2954793028 0.233233018
## 3  3120.000 2.1566820276 1.0000000000 0.6372549020 0.503009458
## 4  4896.000 3.3843317972 1.5692307692 1.0000000000 0.789337919
## 5  6202.667 4.2875576037 1.9880341880 1.2668845316 1.000000000
## 6  8106.667 5.6036866359 2.5982905983 1.6557734205 1.306964746
## 7  7850.667 5.4267281106 2.5162393162 1.6034858388 1.265692175
## 8  9344.000 6.4589861751 2.9948717949 1.9084967320 1.506448839
## 9  7594.667 5.2497695853 2.4341880342 1.5511982571 1.224419604
## 10 6144.000 4.2470046083 1.9692307692 1.2549019608 0.990541702
## 11 3072.000 2.1235023041 0.9846153846 0.6274509804 0.495270851
## 12 3413.333 2.3594470046 1.0940170940 0.6971677560 0.550300946
## 13 1365.333 0.9437788018 0.4376068376 0.2788671024 0.220120378
## 14 2730.667 1.8875576037 0.8752136752 0.5577342048 0.440240757
## 15 5461.333 3.7751152074 1.7504273504 1.1154684096 0.880481513
##               6            7            8            9           10
## 1  0.0001233553 0.0001273777 0.0001070205 0.0001316713 0.0001627604
## 2  0.1784539474 0.1842730978 0.1548230594 0.1904845506 0.2354600694
## 3  0.3848684211 0.3974184783 0.3339041096 0.4108146067 0.5078125000
## 4  0.6039473684 0.6236413043 0.5239726027 0.6446629213 0.7968750000
## 5  0.7651315789 0.7900815217 0.6638127854 0.8167134831 1.0095486111
## 6  1.0000000000 1.0326086957 0.8675799087 1.0674157303 1.3194444444
## 7  0.9684210526 1.0000000000 0.8401826484 1.0337078652 1.2777777778
## 8  1.1526315789 1.1902173913 1.0000000000 1.2303370787 1.5208333333
## 9  0.9368421053 0.9673913043 0.8127853881 1.0000000000 1.2361111111
## 10 0.7578947368 0.7826086957 0.6575342466 0.8089887640 1.0000000000
## 11 0.3789473684 0.3913043478 0.3287671233 0.4044943820 0.5000000000
## 12 0.4210526316 0.4347826087 0.3652968037 0.4494382022 0.5555555556
## 13 0.1684210526 0.1739130435 0.1461187215 0.1797752809 0.2222222222
## 14 0.3368421053 0.3478260870 0.2922374429 0.3595505618 0.4444444444
## 15 0.6736842105 0.6956521739 0.5844748858 0.7191011236 0.8888888889
##              11           12           13           14           15
## 1  0.0003255208 0.0002929688 0.0007324219 0.0003662109 0.0001831055
## 2  0.4709201389 0.4238281250 1.0595703125 0.5297851563 0.2648925781
## 3  1.0156250000 0.9140625000 2.2851562500 1.1425781250 0.5712890625
## 4  1.5937500000 1.4343750000 3.5859375000 1.7929687500 0.8964843750
## 5  2.0190972222 1.8171875000 4.5429687500 2.2714843750 1.1357421875
## 6  2.6388888889 2.3750000000 5.9375000000 2.9687500000 1.4843750000
## 7  2.5555555556 2.3000000000 5.7500000000 2.8750000000 1.4375000000
## 8  3.0416666667 2.7375000000 6.8437500000 3.4218750000 1.7109375000
## 9  2.4722222222 2.2250000000 5.5625000000 2.7812500000 1.3906250000
## 10 2.0000000000 1.8000000000 4.5000000000 2.2500000000 1.1250000000
## 11 1.0000000000 0.9000000000 2.2500000000 1.1250000000 0.5625000000
## 12 1.1111111111 1.0000000000 2.5000000000 1.2500000000 0.6250000000
## 13 0.4444444444 0.4000000000 1.0000000000 0.5000000000 0.2500000000
## 14 0.8888888889 0.8000000000 2.0000000000 1.0000000000 0.5000000000
## 15 1.7777777778 1.6000000000 4.0000000000 2.0000000000 1.0000000000

KUN

##              1           2            3            4          5
## 1     1.000000   0.1021127  0.005484115  0.001942658 0.00108468
## 2     9.793103   1.0000000  0.053706505  0.019024652 0.01062238
## 3   182.344828  18.6197183  1.000000000  0.354233655 0.19778576
## 4   514.758621  52.5633803  2.822995461  1.000000000 0.55834829
## 5   921.931034  94.1408451  5.055975794  1.790996785 1.00000000
## 6  1315.310345 134.3098592  7.213313162  2.555198285 1.42669060
## 7  1600.000000 163.3802817  8.774583964  3.108252947 1.73548773
## 8  2193.655172 224.0000000 12.030257186  4.261521972 2.37941352
## 9  2162.758621 220.8450704 11.860816944  4.201500536 2.34590066
## 10 2560.000000 261.4084507 14.039334342  4.973204716 2.77678037
## 11 2754.206897 281.2394366 15.104387292  5.350482315 2.98743268
## 12 3177.931034 324.5070423 17.428139183  6.173633441 3.44703770
## 13 3248.551724 331.7183099 17.815431165  6.310825295 3.52363854
## 14 3107.310345 317.2957746 17.040847201  6.036441586 3.37043686
## 15 2259.862069 230.7605634 12.393343419  4.390139335 2.45122681
## 16 2259.862069 230.7605634 12.393343419  4.390139335 2.45122681
## 17 6779.586207 692.2816901 37.180030257 13.170418006 7.35368043
## 18 4519.724138 461.5211268 24.786686838  8.780278671 4.90245362
##               6          7            8            9          10
## 1  0.0007602768 0.00062500 0.0004558602 0.0004623724 0.000390625
## 2  0.0074454698 0.00612069 0.0044642857 0.0045280612 0.003825431
## 3  0.1386325503 0.11396552 0.0831237425 0.0843112245 0.071228448
## 4  0.3913590604 0.32172414 0.2346579477 0.2380102041 0.201077586
## 5  0.7009228188 0.57620690 0.4202716298 0.4262755102 0.360129310
## 6  1.0000000000 0.82206897 0.5995975855 0.6081632653 0.513793103
## 7  1.2164429530 1.00000000 0.7293762575 0.7397959184 0.625000000
## 8  1.6677852349 1.37103448 1.0000000000 1.0142857143 0.856896552
## 9  1.6442953020 1.35172414 0.9859154930 1.0000000000 0.844827586
## 10 1.9463087248 1.60000000 1.1670020121 1.1836734694 1.000000000
## 11 2.0939597315 1.72137931 1.2555331992 1.2734693878 1.075862069
## 12 2.4161073826 1.98620690 1.4486921529 1.4693877551 1.241379310
## 13 2.4697986577 2.03034483 1.4808853119 1.5020408163 1.268965517
## 14 2.3624161074 1.94206897 1.4164989940 1.4367346939 1.213793103
## 15 1.7181208054 1.41241379 1.0301810865 1.0448979592 0.882758621
## 16 1.7181208054 1.41241379 1.0301810865 1.0448979592 0.882758621
## 17 5.1543624161 4.23724138 3.0905432596 3.1346938776 2.648275862
## 18 3.4362416107 2.82482759 2.0603621730 2.0897959184 1.765517241
##              11           12           13           14           15
## 1  0.0003630809 0.0003146701 0.0003078295 0.0003218217 0.0004425049
## 2  0.0035556891 0.0030815972 0.0030146060 0.0031516335 0.0043334961
## 3  0.0662059295 0.0573784722 0.0561311141 0.0586825284 0.0806884766
## 4  0.1868990385 0.1619791667 0.1584578804 0.1656605114 0.2277832031
## 5  0.3347355769 0.2901041667 0.2837975543 0.2966974432 0.4079589844
## 6  0.4775641026 0.4138888889 0.4048913043 0.4232954545 0.5820312500
## 7  0.5809294872 0.5034722222 0.4925271739 0.5149147727 0.7080078125
## 8  0.7964743590 0.6902777778 0.6752717391 0.7059659091 0.9707031250
## 9  0.7852564103 0.6805555556 0.6657608696 0.6960227273 0.9570312500
## 10 0.9294871795 0.8055555556 0.7880434783 0.8238636364 1.1328125000
## 11 1.0000000000 0.8666666667 0.8478260870 0.8863636364 1.2187500000
## 12 1.1538461538 1.0000000000 0.9782608696 1.0227272727 1.4062500000
## 13 1.1794871795 1.0222222222 1.0000000000 1.0454545455 1.4375000000
## 14 1.1282051282 0.9777777778 0.9565217391 1.0000000000 1.3750000000
## 15 0.8205128205 0.7111111111 0.6956521739 0.7272727273 1.0000000000
## 16 0.8205128205 0.7111111111 0.6956521739 0.7272727273 1.0000000000
## 17 2.4615384615 2.1333333333 2.0869565217 2.1818181818 3.0000000000
## 18 1.6410256410 1.4222222222 1.3913043478 1.4545454545 2.0000000000
##              16           17           18
## 1  0.0004425049 0.0001475016 0.0002212524
## 2  0.0043334961 0.0014444987 0.0021667480
## 3  0.0806884766 0.0268961589 0.0403442383
## 4  0.2277832031 0.0759277344 0.1138916016
## 5  0.4079589844 0.1359863281 0.2039794922
## 6  0.5820312500 0.1940104167 0.2910156250
## 7  0.7080078125 0.2360026042 0.3540039063
## 8  0.9707031250 0.3235677083 0.4853515625
## 9  0.9570312500 0.3190104167 0.4785156250
## 10 1.1328125000 0.3776041667 0.5664062500
## 11 1.2187500000 0.4062500000 0.6093750000
## 12 1.4062500000 0.4687500000 0.7031250000
## 13 1.4375000000 0.4791666667 0.7187500000
## 14 1.3750000000 0.4583333333 0.6875000000
## 15 1.0000000000 0.3333333333 0.5000000000
## 16 1.0000000000 0.3333333333 0.5000000000
## 17 3.0000000000 1.0000000000 1.5000000000
## 18 2.0000000000 0.6666666667 1.0000000000

LAAO

##              0           1           2            3           4
## 0     1.000000   0.1065089  0.01294964  0.006276151 0.004136029
## 1     9.388889   1.0000000  0.12158273  0.058926081 0.038832721
## 2    77.222222   8.2248521  1.00000000  0.484658298 0.319393382
## 3   159.333333  16.9704142  2.06330935  1.000000000 0.659007353
## 4   241.777778  25.7514793  3.13093525  1.517433752 1.000000000
## 5   353.777778  37.6804734  4.58129496  2.220362622 1.463235294
## 6   392.888889  41.8461538  5.08776978  2.465829847 1.625000000
## 7   394.666667  42.0355030  5.11079137  2.476987448 1.632352941
## 8   440.888889  46.9585799  5.70935252  2.767085077 1.823529412
## 9   369.777778  39.3846154  4.78848921  2.320781032 1.529411765
## 10  284.444444  30.2958580  3.68345324  1.785216179 1.176470588
## 11  341.333333  36.3550296  4.42014388  2.142259414 1.411764706
## 12  341.333333  36.3550296  4.42014388  2.142259414 1.411764706
## 13  227.555556  24.2366864  2.94676259  1.428172943 0.941176471
## 15 1820.444444 193.8934911 23.57410072 11.425383543 7.529411765
##              5           6           7           8           9          10
## 0  0.002826633 0.002545249 0.002533784 0.002268145 0.002704327 0.003515625
## 1  0.026538945 0.023897059 0.023789414 0.021295363 0.025390625 0.033007812
## 2  0.218278894 0.196549774 0.195664414 0.175151210 0.208834135 0.271484375
## 3  0.450376884 0.405542986 0.403716216 0.361391129 0.430889423 0.560156250
## 4  0.683417085 0.615384615 0.612612613 0.548387097 0.653846154 0.850000000
## 5  1.000000000 0.900452489 0.896396396 0.802419355 0.956730769 1.243750000
## 6  1.110552764 1.000000000 0.995495495 0.891129032 1.062500000 1.381250000
## 7  1.115577889 1.004524887 1.000000000 0.895161290 1.067307692 1.387500000
## 8  1.246231156 1.122171946 1.117117117 1.000000000 1.192307692 1.550000000
## 9  1.045226131 0.941176471 0.936936937 0.838709677 1.000000000 1.300000000
## 10 0.804020101 0.723981900 0.720720721 0.645161290 0.769230769 1.000000000
## 11 0.964824121 0.868778281 0.864864865 0.774193548 0.923076923 1.200000000
## 12 0.964824121 0.868778281 0.864864865 0.774193548 0.923076923 1.200000000
## 13 0.643216080 0.579185520 0.576576577 0.516129032 0.615384615 0.800000000
## 15 5.145728643 4.633484163 4.612612613 4.129032258 4.923076923 6.400000000
##             11          12          13           15
## 0  0.002929687 0.002929688 0.004394531 0.0005493164
## 1  0.027506510 0.027506510 0.041259766 0.0051574707
## 2  0.226236979 0.226236979 0.339355469 0.0424194336
## 3  0.466796875 0.466796875 0.700195313 0.0875244141
## 4  0.708333333 0.708333333 1.062500000 0.1328125000
## 5  1.036458333 1.036458333 1.554687500 0.1943359375
## 6  1.151041667 1.151041667 1.726562500 0.2158203125
## 7  1.156250000 1.156250000 1.734375000 0.2167968750
## 8  1.291666667 1.291666667 1.937500000 0.2421875000
## 9  1.083333333 1.083333333 1.625000000 0.2031250000
## 10 0.833333333 0.833333333 1.250000000 0.1562500000
## 11 1.000000000 1.000000000 1.500000000 0.1875000000
## 12 1.000000000 1.000000000 1.500000000 0.1875000000
## 13 0.666666667 0.666666667 1.000000000 0.1250000000
## 15 5.333333333 5.333333333 8.000000000 1.0000000000

vPLA2

##            1          2         3          4          5          6
## 1   1.000000 0.03659081 0.0196737 0.01790393 0.01856884 0.02628205
## 2  27.329268 1.00000000 0.5376679 0.48930131 0.50747283 0.71826923
## 3  50.829268 1.85988398 1.0000000 0.91004367 0.94384058 1.33589744
## 4  55.853659 2.04373048 1.0988484 1.00000000 1.03713768 1.46794872
## 5  53.853659 1.97054886 1.0595010 0.96419214 1.00000000 1.41538462
## 6  38.048780 1.39223561 0.7485605 0.68122271 0.70652174 1.00000000
## 7  29.268293 1.07095047 0.5758157 0.52401747 0.54347826 0.76923077
## 8  24.195122 0.88531905 0.4760077 0.43318777 0.44927536 0.63589744
## 9  14.048780 0.51405622 0.2763916 0.25152838 0.26086957 0.36923077
## 10  9.365854 0.34270415 0.1842610 0.16768559 0.17391304 0.24615385
## 11  6.243902 0.22846943 0.1228407 0.11179039 0.11594203 0.16410256
## 12 12.487805 0.45693887 0.2456814 0.22358079 0.23188406 0.32820513
##             7          8          9        10        11         12
## 1  0.03416667 0.04133065 0.07118056 0.1067708 0.1601562 0.08007813
## 2  0.93375000 1.12953629 1.94531250 2.9179688 4.3769531 2.18847656
## 3  1.73666667 2.10080645 3.61805556 5.4270833 8.1406250 4.07031250
## 4  1.90833333 2.30846774 3.97569444 5.9635417 8.9453125 4.47265625
## 5  1.84000000 2.22580645 3.83333333 5.7500000 8.6250000 4.31250000
## 6  1.30000000 1.57258065 2.70833333 4.0625000 6.0937500 3.04687500
## 7  1.00000000 1.20967742 2.08333333 3.1250000 4.6875000 2.34375000
## 8  0.82666667 1.00000000 1.72222222 2.5833333 3.8750000 1.93750000
## 9  0.48000000 0.58064516 1.00000000 1.5000000 2.2500000 1.12500000
## 10 0.32000000 0.38709677 0.66666667 1.0000000 1.5000000 0.75000000
## 11 0.21333333 0.25806452 0.44444444 0.6666667 1.0000000 0.50000000
## 12 0.42666667 0.51612903 0.88888889 1.3333333 2.0000000 1.00000000

ePLA2

##             1            2            3            4            5
## 1      1.0000   0.02857143  0.001447876 0.0005215577 0.0002741228
## 2     35.0000   1.00000000  0.050675676 0.0182545202 0.0095942982
## 3    690.6667  19.73333333  1.000000000 0.3602225313 0.1893274854
## 4   1917.3333  54.78095238  2.776061776 1.0000000000 0.5255847953
## 5   3648.0000 104.22857143  5.281853282 1.9026425591 1.0000000000
## 6   5269.3333 150.55238095  7.629343629 2.7482614743 1.4444444444
## 7   7050.6667 201.44761905 10.208494208 3.6773296245 1.9327485380
## 8   8746.6667 249.90476190 12.664092664 4.5618915160 2.3976608187
## 9  10453.3333 298.66666667 15.135135135 5.4520166898 2.8654970760
## 10 10069.3333 287.69523810 14.579150579 5.2517385257 2.7602339181
## 11 10581.3333 302.32380952 15.320463320 5.5187760779 2.9005847953
## 12 10922.6667 312.07619048 15.814671815 5.6968011127 2.9941520468
## 13 13653.3333 390.09523810 19.768339768 7.1210013908 3.7426900585
## 14  9557.3333 273.06666667 13.837837838 4.9847009736 2.6198830409
## 15  8192.0000 234.05714286 11.861003861 4.2726008345 2.2456140351
## 16  5461.3333 156.03809524  7.907335907 2.8484005563 1.4970760234
## 17 10922.6667 312.07619048 15.814671815 5.6968011127 2.9941520468
##               6            7            8            9           10
## 1  0.0001897773 0.0001418306 0.0001143293 9.566327e-05 9.931144e-05
## 2  0.0066422065 0.0049640696 0.0040015244 3.348214e-03 3.475900e-03
## 3  0.1310728745 0.0979576399 0.0789634146 6.607143e-02 6.859110e-02
## 4  0.3638663968 0.2719364599 0.2192073171 1.834184e-01 1.904131e-01
## 5  0.6923076923 0.5173978820 0.4170731707 3.489796e-01 3.622881e-01
## 6  1.0000000000 0.7473524962 0.6024390244 5.040816e-01 5.233051e-01
## 7  1.3380566802 1.0000000000 0.8060975610 6.744898e-01 7.002119e-01
## 8  1.6599190283 1.2405446293 1.0000000000 8.367347e-01 8.686441e-01
## 9  1.9838056680 1.4826021180 1.1951219512 1.000000e+00 1.038136e+00
## 10 1.9109311741 1.4281391831 1.1512195122 9.632653e-01 1.000000e+00
## 11 2.0080971660 1.5007564297 1.2097560976 1.012245e+00 1.050847e+00
## 12 2.0728744939 1.5491679274 1.2487804878 1.044898e+00 1.084746e+00
## 13 2.5910931174 1.9364599092 1.5609756098 1.306122e+00 1.355932e+00
## 14 1.8137651822 1.3555219365 1.0926829268 9.142857e-01 9.491525e-01
## 15 1.5546558704 1.1618759455 0.9365853659 7.836735e-01 8.135593e-01
## 16 1.0364372470 0.7745839637 0.6243902439 5.224490e-01 5.423729e-01
## 17 2.0728744939 1.5491679274 1.2487804878 1.044898e+00 1.084746e+00
##              11           12           13           14           15
## 1  9.450605e-05 9.155273e-05 7.324219e-05 0.0001046317 0.0001220703
## 2  3.307712e-03 3.204346e-03 2.563477e-03 0.0036621094 0.0042724609
## 3  6.527218e-02 6.323242e-02 5.058594e-02 0.0722656250 0.0843098958
## 4  1.811996e-01 1.755371e-01 1.404297e-01 0.2006138393 0.2340494792
## 5  3.447581e-01 3.339844e-01 2.671875e-01 0.3816964286 0.4453125000
## 6  4.979839e-01 4.824219e-01 3.859375e-01 0.5513392857 0.6432291667
## 7  6.663306e-01 6.455078e-01 5.164063e-01 0.7377232143 0.8606770833
## 8  8.266129e-01 8.007813e-01 6.406250e-01 0.9151785714 1.0677083333
## 9  9.879032e-01 9.570313e-01 7.656250e-01 1.0937500000 1.2760416667
## 10 9.516129e-01 9.218750e-01 7.375000e-01 1.0535714286 1.2291666667
## 11 1.000000e+00 9.687500e-01 7.750000e-01 1.1071428571 1.2916666667
## 12 1.032258e+00 1.000000e+00 8.000000e-01 1.1428571429 1.3333333333
## 13 1.290323e+00 1.250000e+00 1.000000e+00 1.4285714286 1.6666666667
## 14 9.032258e-01 8.750000e-01 7.000000e-01 1.0000000000 1.1666666667
## 15 7.741935e-01 7.500000e-01 6.000000e-01 0.8571428571 1.0000000000
## 16 5.161290e-01 5.000000e-01 4.000000e-01 0.5714285714 0.6666666667
## 17 1.032258e+00 1.000000e+00 8.000000e-01 1.1428571429 1.3333333333
##              16           17
## 1  0.0001831055 9.155273e-05
## 2  0.0064086914 3.204346e-03
## 3  0.1264648438 6.323242e-02
## 4  0.3510742188 1.755371e-01
## 5  0.6679687500 3.339844e-01
## 6  0.9648437500 4.824219e-01
## 7  1.2910156250 6.455078e-01
## 8  1.6015625000 8.007812e-01
## 9  1.9140625000 9.570313e-01
## 10 1.8437500000 9.218750e-01
## 11 1.9375000000 9.687500e-01
## 12 2.0000000000 1.000000e+00
## 13 2.5000000000 1.250000e+00
## 14 1.7500000000 8.750000e-01
## 15 1.5000000000 7.500000e-01
## 16 1.0000000000 5.000000e-01
## 17 2.0000000000 1.000000e+00

SVMP

##              0           1           2           3           4           5
## 0     1.000000   0.4204545 0.004693049 0.002073061 0.001344477 0.001008944
## 1     2.378378   1.0000000 0.011161847 0.004930524 0.003197674 0.002399651
## 2   213.081081  89.5909091 1.000000000 0.441730166 0.286482558 0.214986911
## 3   482.378378 202.8181818 2.263825469 1.000000000 0.648546512 0.486692845
## 4   743.783784 312.7272727 3.490613902 1.541909458 1.000000000 0.750436300
## 5   991.135135 416.7272727 4.651445967 2.054683998 1.332558140 1.000000000
## 6  1101.837838 463.2727273 5.170979198 2.284177499 1.481395349 1.111692845
## 7  1217.729730 512.0000000 5.714865550 2.524428507 1.637209302 1.228621291
## 8  1300.756757 546.9090909 6.104515474 2.696548633 1.748837209 1.312390925
## 9  1383.783784 581.8181818 6.494165398 2.868668758 1.860465116 1.396160558
## 10 1217.729730 512.0000000 5.714865550 2.524428507 1.637209302 1.228621291
## 11  830.270270 349.0909091 3.896499239 1.721201255 1.116279070 0.837696335
## 12  774.918919 325.8181818 3.636732623 1.606454505 1.041860465 0.781849913
## 13 1328.432432 558.5454545 6.234398782 2.753922008 1.786046512 1.340314136
## 14  885.621622 372.3636364 4.156265855 1.835948005 1.190697674 0.893542757
## 15  885.621622 372.3636364 4.156265855 1.835948005 1.190697674 0.893542757
##               6            7            8            9           10
## 0  0.0009075746 0.0008212003 0.0007687832 0.0007226563 0.0008212003
## 1  0.0021585557 0.0019531250 0.0018284574 0.0017187500 0.0019531250
## 2  0.1933869702 0.1749822443 0.1638131649 0.1539843750 0.1749822443
## 3  0.4377943485 0.3961292614 0.3708444149 0.3485937500 0.3961292614
## 4  0.6750392465 0.6107954545 0.5718085106 0.5375000000 0.6107954545
## 5  0.8995290424 0.8139204545 0.7619680851 0.7162500000 0.8139204545
## 6  1.0000000000 0.9048295455 0.8470744681 0.7962500000 0.9048295455
## 7  1.1051805338 1.0000000000 0.9361702128 0.8800000000 1.0000000000
## 8  1.1805337520 1.0681818182 1.0000000000 0.9400000000 1.0681818182
## 9  1.2558869702 1.1363636364 1.0638297872 1.0000000000 1.1363636364
## 10 1.1051805338 1.0000000000 0.9361702128 0.8800000000 1.0000000000
## 11 0.7535321821 0.6818181818 0.6382978723 0.6000000000 0.6818181818
## 12 0.7032967033 0.6363636364 0.5957446809 0.5600000000 0.6363636364
## 13 1.2056514914 1.0909090909 1.0212765957 0.9600000000 1.0909090909
## 14 0.8037676609 0.7272727273 0.6808510638 0.6400000000 0.7272727273
## 15 0.8037676609 0.7272727273 0.6808510638 0.6400000000 0.7272727273
##             11          12           13          14          15
## 0  0.001204427 0.001290458 0.0007527669 0.001129150 0.001129150
## 1  0.002864583 0.003069196 0.0017903646 0.002685547 0.002685547
## 2  0.256640625 0.274972098 0.1604003906 0.240600586 0.240600586
## 3  0.580989583 0.622488839 0.3631184896 0.544677734 0.544677734
## 4  0.895833333 0.959821429 0.5598958333 0.839843750 0.839843750
## 5  1.193750000 1.279017857 0.7460937500 1.119140625 1.119140625
## 6  1.327083333 1.421875000 0.8294270833 1.244140625 1.244140625
## 7  1.466666667 1.571428571 0.9166666667 1.375000000 1.375000000
## 8  1.566666667 1.678571429 0.9791666667 1.468750000 1.468750000
## 9  1.666666667 1.785714286 1.0416666667 1.562500000 1.562500000
## 10 1.466666667 1.571428571 0.9166666667 1.375000000 1.375000000
## 11 1.000000000 1.071428571 0.6250000000 0.937500000 0.937500000
## 12 0.933333333 1.000000000 0.5833333333 0.875000000 0.875000000
## 13 1.600000000 1.714285714 1.0000000000 1.500000000 1.500000000
## 14 1.066666667 1.142857143 0.6666666667 1.000000000 1.000000000
## 15 1.066666667 1.142857143 0.6666666667 1.000000000 1.000000000

SVSP

##            2           3          4          5          6           7
## 2    1.00000  0.09135802 0.02617925 0.01359628 0.01003254 0.008575402
## 3   10.94595  1.00000000 0.28655660 0.14882411 0.10981562 0.093865884
## 4   38.19820  3.48971193 1.00000000 0.51935326 0.38322487 0.327564895
## 5   73.54955  6.71934156 1.92547170 1.00000000 0.73788865 0.630716934
## 6   99.67568  9.10617284 2.60943396 1.35521803 1.00000000 0.854758962
## 7  116.61261 10.65349794 3.05283019 1.58549731 1.16992046 1.000000000
## 8  113.87387 10.40329218 2.98113208 1.54826066 1.14244396 0.976514215
## 9  107.81982  9.85020576 2.82264151 1.46594806 1.08170644 0.924598269
## 10  85.33333  7.79588477 2.23396226 1.16021558 0.85610991 0.731767614
## 11  85.33333  7.79588477 2.23396226 1.16021558 0.85610991 0.731767614
## 12  36.90090  3.37119342 0.96603774 0.50171485 0.37020969 0.316440049
## 13  64.57658  5.89958848 1.69056604 0.87800098 0.64786696 0.553770087
## 14  18.45045  1.68559671 0.48301887 0.25085742 0.18510484 0.158220025
## 15  73.80180  6.74238683 1.93207547 1.00342969 0.74041938 0.632880099
##              8           9         10         11         12         13
## 2  0.008781646 0.009274733 0.01171875 0.01171875 0.02709961 0.01548549
## 3  0.096123418 0.101520722 0.12827280 0.12827280 0.29663086 0.16950335
## 4  0.335443038 0.354278075 0.44763514 0.44763514 1.03515625 0.59151786
## 5  0.645886076 0.682152406 0.86190878 0.86190878 1.99316406 1.13895089
## 6  0.875316456 0.924465241 1.16807432 1.16807432 2.70117188 1.54352679
## 7  1.024050633 1.081550802 1.36655405 1.36655405 3.16015625 1.80580357
## 8  1.000000000 1.056149733 1.33445946 1.33445946 3.08593750 1.76339286
## 9  0.946835443 1.000000000 1.26351351 1.26351351 2.92187500 1.66964286
## 10 0.749367089 0.791443850 1.00000000 1.00000000 2.31250000 1.32142857
## 11 0.749367089 0.791443850 1.00000000 1.00000000 2.31250000 1.32142857
## 12 0.324050633 0.342245989 0.43243243 0.43243243 1.00000000 0.57142857
## 13 0.567088608 0.598930481 0.75675676 0.75675676 1.75000000 1.00000000
## 14 0.162025316 0.171122995 0.21621622 0.21621622 0.50000000 0.28571429
## 15 0.648101266 0.684491979 0.86486486 0.86486486 2.00000000 1.14285714
##            14        15
## 2  0.05419922 0.0135498
## 3  0.59326172 0.1483154
## 4  2.07031250 0.5175781
## 5  3.98632813 0.9965820
## 6  5.40234375 1.3505859
## 7  6.32031250 1.5800781
## 8  6.17187500 1.5429688
## 9  5.84375000 1.4609375
## 10 4.62500000 1.1562500
## 11 4.62500000 1.1562500
## 12 2.00000000 0.5000000
## 13 3.50000000 0.8750000
## 14 1.00000000 0.2500000
## 15 4.00000000 1.0000000

TFTx

##            2          3         4          5          6          7
## 2   1.000000  0.2439024 0.1100811 0.06384409 0.04576108 0.03971572
## 3   4.100000  1.0000000 0.4513326 0.26176075 0.18762042 0.16283445
## 4   9.084211  2.2156611 1.0000000 0.57997312 0.41570328 0.36078595
## 5  15.663158  3.8202824 1.7242178 1.00000000 0.71676301 0.62207358
## 6  21.852632  5.3299101 2.4055620 1.39516129 1.00000000 0.86789298
## 7  25.178947  6.1412067 2.7717265 1.60752688 1.15221580 1.00000000
## 8  33.010526  8.0513479 3.6338355 2.10752688 1.51059730 1.31103679
## 9  36.378947  8.8729140 4.0046350 2.32258065 1.66473988 1.44481605
## 10 43.115789 10.5160462 4.7462341 2.75268817 1.97302505 1.71237458
## 11 41.768421 10.1874198 4.5979143 2.66666667 1.91136802 1.65886288
## 12 24.252632  5.9152760 2.6697567 1.54838710 1.10982659 0.96321070
## 13 21.557895  5.2580231 2.3731170 1.37634409 0.98651252 0.85618729
## 14 21.557895  5.2580231 2.3731170 1.37634409 0.98651252 0.85618729
## 15 43.115789 10.5160462 4.7462341 2.75268817 1.97302505 1.71237458
## 16 43.115789 10.5160462 4.7462341 2.75268817 1.97302505 1.71237458
##             8          9         10         11         12         13
## 2  0.03029337 0.02748843 0.02319336 0.02394153 0.04123264 0.04638672
## 3  0.12420281 0.11270255 0.09509277 0.09816028 0.16905382 0.19018555
## 4  0.27519133 0.24971065 0.21069336 0.21748992 0.37456597 0.42138672
## 5  0.47448980 0.43055556 0.36328125 0.37500000 0.64583333 0.72656250
## 6  0.66198980 0.60069444 0.50683594 0.52318548 0.90104167 1.01367188
## 7  0.76275510 0.69212963 0.58398437 0.60282258 1.03819444 1.16796875
## 8  1.00000000 0.90740741 0.76562500 0.79032258 1.36111111 1.53125000
## 9  1.10204082 1.00000000 0.84375000 0.87096774 1.50000000 1.68750000
## 10 1.30612245 1.18518519 1.00000000 1.03225806 1.77777778 2.00000000
## 11 1.26530612 1.14814815 0.96875000 1.00000000 1.72222222 1.93750000
## 12 0.73469388 0.66666667 0.56250000 0.58064516 1.00000000 1.12500000
## 13 0.65306122 0.59259259 0.50000000 0.51612903 0.88888889 1.00000000
## 14 0.65306122 0.59259259 0.50000000 0.51612903 0.88888889 1.00000000
## 15 1.30612245 1.18518519 1.00000000 1.03225806 1.77777778 2.00000000
## 16 1.30612245 1.18518519 1.00000000 1.03225806 1.77777778 2.00000000
##            14         15         16
## 2  0.04638672 0.02319336 0.02319336
## 3  0.19018555 0.09509277 0.09509277
## 4  0.42138672 0.21069336 0.21069336
## 5  0.72656250 0.36328125 0.36328125
## 6  1.01367188 0.50683594 0.50683594
## 7  1.16796875 0.58398438 0.58398438
## 8  1.53125000 0.76562500 0.76562500
## 9  1.68750000 0.84375000 0.84375000
## 10 2.00000000 1.00000000 1.00000000
## 11 1.93750000 0.96875000 0.96875000
## 12 1.12500000 0.56250000 0.56250000
## 13 1.00000000 0.50000000 0.50000000
## 14 1.00000000 0.50000000 0.50000000
## 15 2.00000000 1.00000000 1.00000000
## 16 2.00000000 1.00000000 1.00000000

Plotting BAMM data

BPP

edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/BPP/edata_BPP.rds", burnin = 0.1, type= 'diversification')
plot.bammdata(edata, lwd = 1.5, legend = T,labels = T)

distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)

cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 87 plots

cred_Shift$number.distinct
## [1] 91
summary(cred_Shift)
## 
##  95 % credible set of rate shift configurations sampled with BAMM
## 
## Distinct shift configurations in credible set:  91
## 
## Frequency of 9 shift configurations with highest posterior probability:
## 
## 
##    rank     probability cumulative  Core_shifts
##          1 0.22738631  0.2273863          3
##          2 0.09245377  0.3198401          3
##          3 0.09245377  0.4122939          4
##          4 0.05897051  0.4712644          4
##          5 0.03648176  0.5077461          4
##          6 0.03098451  0.5387306          4
##          7 0.03048476  0.5692154          4
##          8 0.02948526  0.5987006          5
##          9 0.02898551  0.6276862          3
## 
## ...omitted 82 additional distinct shift configurations
## from the credible set. You can access the full set from your 
## credibleshiftset object
dev.off()
## null device 
##           1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
## 
## Discarded as burnin: GENERATIONS <  0
## Analyzing  1  samples from posterior
## 
## Setting recursive sequence on tree...
## 
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5, method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator

CRISP

edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/CRISP/edata_CRISP.rds", burnin = 0.1, type= 'diversification')
plot.bammdata(edata, lwd = 1.5, legend = T,labels = T)

distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)

cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 8 plots

cred_Shift$number.distinct
## [1] 12
summary(cred_Shift)
## 
##  95 % credible set of rate shift configurations sampled with BAMM
## 
## Distinct shift configurations in credible set:  12
## 
## Frequency of 9 shift configurations with highest posterior probability:
## 
## 
##    rank     probability cumulative  Core_shifts
##          1 0.37607799  0.3760780          1
##          2 0.16535433  0.5414323          1
##          3 0.12773403  0.6691664          1
##          4 0.09423822  0.7634046          2
##          5 0.06411699  0.8275216          1
##          6 0.03212098  0.8596425          2
##          7 0.02887139  0.8885139          2
##          8 0.02737158  0.9158855          2
##          9 0.01449819  0.9303837          2
## 
## ...omitted 3 additional distinct shift configurations
## from the credible set. You can access the full set from your 
## credibleshiftset object
dev.off()
## null device 
##           1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
## 
## Discarded as burnin: GENERATIONS <  0
## Analyzing  1  samples from posterior
## 
## Setting recursive sequence on tree...
## 
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks", method = 'polar') + addBAMMshifts(best, cex = 2.5, method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator

CTL

edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/CTL/event_dataCTL.txt", burnin = 0.1, type= 'diversification')
plot.bammdata(edata, lwd = 1.5, legend = T,labels = T)

distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)

cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 139 plots

cred_Shift$number.distinct
## [1] 143
summary(cred_Shift)
## 
##  95 % credible set of rate shift configurations sampled with BAMM
## 
## Distinct shift configurations in credible set:  143
## 
## Frequency of 9 shift configurations with highest posterior probability:
## 
## 
##    rank     probability cumulative  Core_shifts
##          1 0.18986779  0.1898678          3
##          2 0.12143095  0.3112987          2
##          3 0.07076991  0.3820687          3
##          4 0.06354849  0.4456172          3
##          5 0.04655038  0.4921675          3
##          6 0.04243973  0.5346073          2
##          7 0.03188535  0.5664926          4
##          8 0.02210865  0.5886013          3
##          9 0.01733141  0.6059327          4
## 
## ...omitted 134 additional distinct shift configurations
## from the credible set. You can access the full set from your 
## credibleshiftset object
dev.off()
## null device 
##           1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
## 
## Discarded as burnin: GENERATIONS <  0
## Analyzing  1  samples from posterior
## 
## Setting recursive sequence on tree...
## 
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator

GF

edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/GF/event_dataGF.txt", burnin = 0.1, type= 'diversification')
plot.bammdata(edata, lwd = 1.5, legend = T,labels = T)

distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)

cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 110 plots

cred_Shift$number.distinct
## [1] 114
summary(cred_Shift)
## 
##  95 % credible set of rate shift configurations sampled with BAMM
## 
## Distinct shift configurations in credible set:  114
## 
## Frequency of 9 shift configurations with highest posterior probability:
## 
## 
##    rank     probability cumulative  Core_shifts
##          1 0.25452727  0.2545273          2
##          2 0.17298078  0.4275081          2
##          3 0.05799356  0.4855016          2
##          4 0.05754916  0.5430508          2
##          5 0.04221753  0.5852683          2
##          6 0.03910677  0.6243751          4
##          7 0.02377514  0.6481502          3
##          8 0.02377514  0.6719253          3
##          9 0.02321964  0.6951450          3
## 
## ...omitted 105 additional distinct shift configurations
## from the credible set. You can access the full set from your 
## credibleshiftset object
dev.off()
## null device 
##           1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
## 
## Discarded as burnin: GENERATIONS <  0
## Analyzing  1  samples from posterior
## 
## Setting recursive sequence on tree...
## 
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator

KSPI

edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/KUN/event_dataKUN.txt", burnin = 0.1, type= 'diversification')
plot.bammdata(edata, lwd = 1.5, legend = T,labels = T)

distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)

cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 317 plots

cred_Shift$number.distinct
## [1] 321
summary(cred_Shift)
## 
##  95 % credible set of rate shift configurations sampled with BAMM
## 
## Distinct shift configurations in credible set:  321
## 
## Frequency of 9 shift configurations with highest posterior probability:
## 
## 
##    rank     probability cumulative  Core_shifts
##          1 0.23447069  0.2344707          3
##          2 0.09123860  0.3257093          3
##          3 0.05436820  0.3800775          4
##          4 0.03237095  0.4124484          3
##          5 0.03187102  0.4443195          4
##          6 0.02824647  0.4725659          4
##          7 0.02287214  0.4954381          3
##          8 0.01987252  0.5153106          3
##          9 0.01424822  0.5295588          3
## 
## ...omitted 312 additional distinct shift configurations
## from the credible set. You can access the full set from your 
## credibleshiftset object
dev.off()
## null device 
##           1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
## 
## Discarded as burnin: GENERATIONS <  0
## Analyzing  1  samples from posterior
## 
## Setting recursive sequence on tree...
## 
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator

LAAO

edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/LAAO/event_dataLAAO.txt", burnin = 0.1, type= 'diversification')
plot.bammdata(edata, lwd = 1.5, legend = T,labels = T)

distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)

cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 42 plots

cred_Shift$number.distinct
## [1] 46
summary(cred_Shift)
## 
##  95 % credible set of rate shift configurations sampled with BAMM
## 
## Distinct shift configurations in credible set:  46
## 
## Frequency of 9 shift configurations with highest posterior probability:
## 
## 
##    rank     probability cumulative  Core_shifts
##          1 0.23058980  0.2305898          2
##          2 0.11262912  0.3432189          2
##          3 0.11262912  0.4558481          2
##          4 0.06864379  0.5244918          0
##          5 0.05598134  0.5804732          3
##          6 0.04798401  0.6284572          2
##          7 0.04265245  0.6711096          1
##          8 0.02765745  0.6987671          2
##          9 0.02465845  0.7234255          3
## 
## ...omitted 37 additional distinct shift configurations
## from the credible set. You can access the full set from your 
## credibleshiftset object
dev.off()
## null device 
##           1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
## 
## Discarded as burnin: GENERATIONS <  0
## Analyzing  1  samples from posterior
## 
## Setting recursive sequence on tree...
## 
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator

vPLA2

edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/vPLA2ePLA2/event_data_vPLA2.txt", burnin = 0.1, type= 'diversification')
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)

cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 9 plots

cred_Shift$number.distinct
## [1] 13
summary(cred_Shift)
## 
##  95 % credible set of rate shift configurations sampled with BAMM
## 
## Distinct shift configurations in credible set:  13
## 
## Frequency of 9 shift configurations with highest posterior probability:
## 
## 
##    rank     probability cumulative  Core_shifts
##          1 0.56805399  0.5680540          2
##          2 0.16222972  0.7302837          3
##          3 0.04911886  0.7794026          3
##          4 0.04424447  0.8236470          1
##          5 0.02612173  0.8497688          2
##          6 0.02124734  0.8710161          4
##          7 0.02037245  0.8913886          1
##          8 0.01687289  0.9082615          2
##          9 0.01399825  0.9222597          3
## 
## ...omitted 4 additional distinct shift configurations
## from the credible set. You can access the full set from your 
## credibleshiftset object
dev.off()
## null device 
##           1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
## 
## Discarded as burnin: GENERATIONS <  0
## Analyzing  1  samples from posterior
## 
## Setting recursive sequence on tree...
## 
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator

ePLA2

edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/vPLA2ePLA2/event_data_ePLA2.txt", burnin = 0.1, type= 'diversification')
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)

cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 352 plots

cred_Shift$number.distinct
## [1] 356
summary(cred_Shift)
## 
##  95 % credible set of rate shift configurations sampled with BAMM
## 
## Distinct shift configurations in credible set:  356
## 
## Frequency of 9 shift configurations with highest posterior probability:
## 
## 
##    rank     probability cumulative  Core_shifts
##          1 0.14885639  0.1488564          3
##          2 0.10323710  0.2520935          3
##          3 0.06249219  0.3145857          4
##          4 0.05311836  0.3677040          3
##          5 0.02987127  0.3975753          3
##          6 0.02849644  0.4260717          3
##          7 0.02412198  0.4501937          4
##          8 0.02374703  0.4739408          4
##          9 0.01887264  0.4928134          3
## 
## ...omitted 347 additional distinct shift configurations
## from the credible set. You can access the full set from your 
## credibleshiftset object
dev.off()
## null device 
##           1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
## 
## Discarded as burnin: GENERATIONS <  0
## Analyzing  1  samples from posterior
## 
## Setting recursive sequence on tree...
## 
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator

SVMP

edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/SVMP/event_dataSVMP.txt", burnin = 0.1, type= 'diversification')
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)

cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 0 plots

cred_Shift$number.distinct
## [1] 4
summary(cred_Shift)
## 
##  95 % credible set of rate shift configurations sampled with BAMM
## 
## Distinct shift configurations in credible set:  4
## 
## Frequency of 4 shift configurations with highest posterior probability:
## 
## 
##    rank     probability cumulative  Core_shifts
##          1 0.84672391  0.8467239          2
##          2 0.05599341  0.9027173          3
##          3 0.03623103  0.9389484          3
##          4 0.02929067  0.9682390          3
dev.off()
## null device 
##           1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
## 
## Discarded as burnin: GENERATIONS <  0
## Analyzing  1  samples from posterior
## 
## Setting recursive sequence on tree...
## 
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator

SVSP

edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/SVSP/event_dataLAAO.txt", burnin = 0.1, type= 'diversification')
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)

cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 36 plots

cred_Shift$number.distinct
## [1] 40
summary(cred_Shift)
## 
##  95 % credible set of rate shift configurations sampled with BAMM
## 
## Distinct shift configurations in credible set:  40
## 
## Frequency of 9 shift configurations with highest posterior probability:
## 
## 
##    rank     probability cumulative  Core_shifts
##          1 0.18821315  0.1882132          4
##          2 0.16303964  0.3512528          3
##          3 0.10692860  0.4581814          4
##          4 0.09398894  0.5521703          3
##          5 0.04246559  0.5946359          2
##          6 0.04070109  0.6353370          3
##          7 0.03093754  0.6662746          5
##          8 0.03034937  0.6966239          5
##          9 0.02623221  0.7228561          4
## 
## ...omitted 31 additional distinct shift configurations
## from the credible set. You can access the full set from your 
## credibleshiftset object
dev.off()
## null device 
##           1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
## 
## Discarded as burnin: GENERATIONS <  0
## Analyzing  1  samples from posterior
## 
## Setting recursive sequence on tree...
## 
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator

TFTx

edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/TFTx/event_dataTFTx.txt", burnin = 0.1, type= 'diversification')
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)

cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 139 plots

cred_Shift$number.distinct
## [1] 143
summary(cred_Shift)
## 
##  95 % credible set of rate shift configurations sampled with BAMM
## 
## Distinct shift configurations in credible set:  143
## 
## Frequency of 9 shift configurations with highest posterior probability:
## 
## 
##    rank     probability cumulative  Core_shifts
##          1 0.17520620  0.1752062          2
##          2 0.17270682  0.3479130          3
##          3 0.07273182  0.4206448          2
##          4 0.05723569  0.4778805          4
##          5 0.04098975  0.5188703          4
##          6 0.03924019  0.5581105          3
##          7 0.02624344  0.5843539          3
##          8 0.02549363  0.6098475          3
##          9 0.01599600  0.6258435          4
## 
## ...omitted 134 additional distinct shift configurations
## from the credible set. You can access the full set from your 
## credibleshiftset object
dev.off()
## null device 
##           1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
## 
## Discarded as burnin: GENERATIONS <  0
## Analyzing  1  samples from posterior
## 
## Setting recursive sequence on tree...
## 
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator

Rate through time

Since the early burst model states that branching events account for most of the phenotypic diversity amongst species (Simpson 1953.; Ingram et al. 2012), we expect the rate of trait evolution to be high immediately after major lineages diverge. To identify these increases we estimated the evolutionary rate of each toxin family after the split of the three venomous families. Our estimates of ‘rate through time’ revealed that toxin families show unique evolutionary rates and rate dynamics in each venomous snake family (Fig. 4)

BPP

st <- max(branching.times(tree))
plotRateThroughTime(edataBPP, intervalCol="blue", avgCol="blue", start.time=st, node=97, ylim=c(0,.08),cex.axis=1)+
text(x=30, y= 0.008, label="Colubrids only", font=4, cex=2.0, pos=4)
plotRateThroughTime(edataBPP, intervalCol="red", avgCol="red", start.time=st, node=54, ylim=c(0,.08),cex.axis=1)+
text(x=30, y= 0.008, label="Vipers only", font=4, cex=2.0, pos=4)
plotRateThroughTime(edataBPP, intervalCol="green", avgCol="green", start.time=st, node=85, ylim=c(0,.08),cex.axis=1)+
text(x=30, y= 0.008, label="Elapids only", font=4, cex=2.0, pos=4)

## integer(0)

## integer(0)

## integer(0)

CRISP

## integer(0)

## integer(0)

## integer(0)

CTL

## integer(0)

## integer(0)

## integer(0)

GF

## integer(0)

## integer(0)

## integer(0)

KSPI

## integer(0)

## integer(0)

## integer(0)

LAAO

## integer(0)

## integer(0)

## integer(0)

vPLA2

## integer(0)

## integer(0)

## integer(0)

ePLA2

## integer(0)

## integer(0)

## integer(0)

SVMP

## integer(0)

## integer(0)

SVSP

## integer(0)

## integer(0)

TFTx

## integer(0)

## integer(0)

Evoluionary models using geiger

We fit a number of trait evolution models to our data to understand which evolutionary process best describes snake venom evolution. Along with conventional models, like Brownian motion (BM), Ornstein-Uhlenbeck (OU), we tested a specific Early burst (EB) model implemented in geiger (Pennell et al. 2014).

Load libraries

library(geiger)
library(phytools)

Evolution models using fitContinuous from geiger

Load data

tree<-read.newick("./Final_tree.tre")
trait<-read.csv("./data/scaleddata/scaled_data_fot_dtt.csv", row.names = 1, header = T)

BPP.CNP

dat<-setNames(trait$BPP.CNP,rownames(trait))

fitBM<-fitContinuous(tree,dat)
fitOU<-fitContinuous(tree,dat,model="OU")
fitEB<-fitContinuous(tree,dat,model="EB")

BM model

fitBM$opt
## $sigsq
## [1] 0.03763935
## 
## $z0
## [1] -0.235386
## 
## $lnL
## [1] -70.77994
## 
## $method
## [1] "Brent"
## 
## $k
## [1] 2
## 
## $aic
## [1] 145.5599
## 
## $aicc
## [1] 145.8048

OU model

fitOU$opt
## $alpha
## [1] 2.718282
## 
## $sigsq
## [1] 2.805926
## 
## $z0
## [1] -0.05130243
## 
## $lnL
## [1] -56.58804
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 119.1761
## 
## $aicc
## [1] 119.6761

EB model

fitEB$opt
## $a
## [1] -1e-06
## 
## $sigsq
## [1] 0.03764146
## 
## $z0
## [1] -0.2353863
## 
## $lnL
## [1] -70.78014
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 147.5603
## 
## $aicc
## [1] 148.0603

AIC

aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),c("BM","OU","EB"))
aic.vals
##       BM       OU       EB 
## 145.8048 119.6761 148.0603

weighted AIC

aic.w(aic.vals)
##         BM         OU         EB 
## 0.00000212 0.99999719 0.00000069


CRISP

BM model

fitBM$opt
## $sigsq
## [1] 0.00281511
## 
## $z0
## [1] -0.2990053
## 
## $lnL
## [1] -3.36067
## 
## $method
## [1] "Brent"
## 
## $k
## [1] 2
## 
## $aic
## [1] 10.72134
## 
## $aicc
## [1] 10.96624

OU model

fitOU$opt
## $alpha
## [1] 0.09424551
## 
## $sigsq
## [1] 0.010191
## 
## $z0
## [1] -0.3486082
## 
## $lnL
## [1] 3.560175
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] -1.12035
## 
## $aicc
## [1] -0.6203504

EB model

fitEB$opt
## $a
## [1] -1e-06
## 
## $sigsq
## [1] 0.002815263
## 
## $z0
## [1] -0.2990054
## 
## $lnL
## [1] -3.360821
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 12.72164
## 
## $aicc
## [1] 13.22164

AIC

aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),c("BM","OU","EB"))
aic.vals
##         BM         OU         EB 
## 10.9662381 -0.6203504 13.2216415

weighted AIC

aic.w(aic.vals)
##         BM         OU         EB 
## 0.00303568 0.99598144 0.00098288


CTL

BM model

fitBM$opt
## $sigsq
## [1] 0.00965261
## 
## $z0
## [1] -0.1509853
## 
## $lnL
## [1] -35.39857
## 
## $method
## [1] "Brent"
## 
## $k
## [1] 2
## 
## $aic
## [1] 74.79714
## 
## $aicc
## [1] 75.04204

OU model

fitOU$opt
## $alpha
## [1] 0.04778383
## 
## $sigsq
## [1] 0.02154569
## 
## $z0
## [1] -0.172549
## 
## $lnL
## [1] -30.58365
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 67.16731
## 
## $aicc
## [1] 67.66731

EB model

fitEB$opt
## $a
## [1] -1e-06
## 
## $sigsq
## [1] 0.009653122
## 
## $z0
## [1] -0.150985
## 
## $lnL
## [1] -35.39869
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 76.79738
## 
## $aicc
## [1] 77.29738

AIC

aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),c("BM","OU","EB"))
aic.vals
##       BM       OU       EB 
## 75.04204 67.66731 77.29738

weighted AIC

aic.w(aic.vals)
##         BM         OU         EB 
## 0.02423460 0.96791855 0.00784685


GF

BM model

fitBM$opt
## $sigsq
## [1] 0.00559709
## 
## $z0
## [1] -0.3978027
## 
## $lnL
## [1] -21.22905
## 
## $method
## [1] "Brent"
## 
## $k
## [1] 2
## 
## $aic
## [1] 46.45811
## 
## $aicc
## [1] 46.70301

OU model

fitOU$opt
## $alpha
## [1] 2.718282
## 
## $sigsq
## [1] 0.4569515
## 
## $z0
## [1] -0.3991772
## 
## $lnL
## [1] -9.400349
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 24.8007
## 
## $aicc
## [1] 25.3007

EB model

fitEB$opt
## $a
## [1] -1e-06
## 
## $sigsq
## [1] 0.005597395
## 
## $z0
## [1] -0.3978025
## 
## $lnL
## [1] -21.22921
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 48.45842
## 
## $aicc
## [1] 48.95842

AIC

aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
                   c("BM","OU","EB"))
aic.vals
##       BM       OU       EB 
## 46.70301 25.30070 48.95842

weighted AIC

aic.w(aic.vals)
##         BM         OU         EB 
## 0.00002252 0.99997019 0.00000729


KSPI

BM model

fitBM$opt
## $sigsq
## [1] 0.0066864
## 
## $z0
## [1] -0.2439804
## 
## $lnL
## [1] -25.8526
## 
## $method
## [1] "Brent"
## 
## $k
## [1] 2
## 
## $aic
## [1] 55.70521
## 
## $aicc
## [1] 55.95011

OU model

fitOU$opt
## $alpha
## [1] 3.115799e-17
## 
## $sigsq
## [1] 0.006686401
## 
## $z0
## [1] -0.2439804
## 
## $lnL
## [1] -25.8526
## 
## $method
## [1] "subplex"
## 
## $k
## [1] 3
## 
## $aic
## [1] 57.70521
## 
## $aicc
## [1] 58.20521

EB model

fitEB$opt
## $a
## [1] -0.0007395406
## 
## $sigsq
## [1] 0.006929684
## 
## $z0
## [1] -0.2440186
## 
## $lnL
## [1] -25.85224
## 
## $method
## [1] "subplex"
## 
## $k
## [1] 3
## 
## $aic
## [1] 57.70449
## 
## $aicc
## [1] 58.20449

AIC

aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
                   c("BM","OU","EB"))
aic.vals
##       BM       OU       EB 
## 55.95011 58.20521 58.20449

weighted AIC

aic.w(aic.vals)
##        BM        OU        EB 
## 0.6068818 0.1965237 0.1965946


LAAO

BM model

fitBM$opt
## $sigsq
## [1] 0.001368342
## 
## $z0
## [1] -0.3831869
## 
## $lnL
## [1] 15.39577
## 
## $method
## [1] "Brent"
## 
## $k
## [1] 2
## 
## $aic
## [1] -26.79153
## 
## $aicc
## [1] -26.54663

OU model

fitOU$opt
## $alpha
## [1] 0.2403901
## 
## $sigsq
## [1] 0.0104923
## 
## $z0
## [1] -0.3780048
## 
## $lnL
## [1] 25.8697
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] -45.7394
## 
## $aicc
## [1] -45.2394

EB model

fitEB$opt
## $a
## [1] -1e-06
## 
## $sigsq
## [1] 0.001368417
## 
## $z0
## [1] -0.3831867
## 
## $lnL
## [1] 15.39561
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] -24.79121
## 
## $aicc
## [1] -24.29121

AIC

aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
                   c("BM","OU","EB"))
aic.vals
##        BM        OU        EB 
## -26.54663 -45.23940 -24.29121

weighted AIC

aic.w(aic.vals)
##         BM         OU         EB 
## 0.00008727 0.99988447 0.00002826


SVMP

BM model

fitBM$opt
## $sigsq
## [1] 0.04095841
## 
## $z0
## [1] 1.335358
## 
## $lnL
## [1] -72.97712
## 
## $method
## [1] "Brent"
## 
## $k
## [1] 2
## 
## $aic
## [1] 149.9542
## 
## $aicc
## [1] 150.1991

OU model

fitOU$opt
## $alpha
## [1] 0.007577426
## 
## $sigsq
## [1] 0.04895337
## 
## $z0
## [1] 1.296654
## 
## $lnL
## [1] -72.64896
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 151.2979
## 
## $aicc
## [1] 151.7979

EB model

fitEB$opt
## $a
## [1] -1e-06
## 
## $sigsq
## [1] 0.04096046
## 
## $z0
## [1] 1.335361
## 
## $lnL
## [1] -72.97717
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 151.9543
## 
## $aicc
## [1] 152.4543

AIC

aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
                   c("BM","OU","EB"))
aic.vals
##       BM       OU       EB 
## 150.1991 151.7979 152.4543

weighted AIC

aic.w(aic.vals)
##        BM        OU        EB 
## 0.5638843 0.2535236 0.1825921


SVSP

BM model

fitBM$opt
## $sigsq
## [1] 0.05996723
## 
## $z0
## [1] 0.007962384
## 
## $lnL
## [1] -82.88939
## 
## $method
## [1] "Brent"
## 
## $k
## [1] 2
## 
## $aic
## [1] 169.7788
## 
## $aicc
## [1] 170.0237

OU model

fitOU$opt
## $alpha
## [1] 2.718282
## 
## $sigsq
## [1] 4.804233
## 
## $z0
## [1] 0.2278837
## 
## $lnL
## [1] -70.56991
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 147.1398
## 
## $aicc
## [1] 147.6398

EB model

fitEB$opt
## $a
## [1] -1e-06
## 
## $sigsq
## [1] 0.0599706
## 
## $z0
## [1] 0.007962912
## 
## $lnL
## [1] -82.88959
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 171.7792
## 
## $aicc
## [1] 172.2792

AIC

aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
                   c("BM","OU","EB"))
aic.vals
##       BM       OU       EB 
## 170.0237 147.6398 172.2792

weighted AIC

aic.w(aic.vals)
##         BM         OU         EB 
## 0.00001378 0.99998175 0.00000446


TFTx

BM model

fitBM$opt
## $sigsq
## [1] 0.02698684
## 
## $z0
## [1] 0.5005985
## 
## $lnL
## [1] -62.12972
## 
## $method
## [1] "Brent"
## 
## $k
## [1] 2
## 
## $aic
## [1] 128.2594
## 
## $aicc
## [1] 128.5043

OU model

fitOU$opt
## $alpha
## [1] 0.003028001
## 
## $sigsq
## [1] 0.0290781
## 
## $z0
## [1] 0.5128266
## 
## $lnL
## [1] -62.0485
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 130.097
## 
## $aicc
## [1] 130.597

EB model

fitEB$opt
## $a
## [1] -1e-06
## 
## $sigsq
## [1] 0.02698818
## 
## $z0
## [1] 0.5005965
## 
## $lnL
## [1] -62.12974
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 130.2595
## 
## $aicc
## [1] 130.7595

AIC

aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
                   c("BM","OU","EB"))
aic.vals
##       BM       OU       EB 
## 128.5043 130.5970 130.7595

weighted AIC

aic.w(aic.vals)
##        BM        OU        EB 
## 0.5970005 0.2096809 0.1933187


vPLA2

BM model

fitBM$opt
## $sigsq
## [1] 0.04813505
## 
## $z0
## [1] -0.1281526
## 
## $lnL
## [1] -77.17491
## 
## $method
## [1] "Brent"
## 
## $k
## [1] 2
## 
## $aic
## [1] 158.3498
## 
## $aicc
## [1] 158.5947

OU model

fitOU$opt
## $alpha
## [1] 0.04565845
## 
## $sigsq
## [1] 0.09045466
## 
## $z0
## [1] -0.07190474
## 
## $lnL
## [1] -68.75383
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 143.5077
## 
## $aicc
## [1] 144.0077

EB model

fitEB$opt
## $a
## [1] -1e-06
## 
## $sigsq
## [1] 0.04813773
## 
## $z0
## [1] -0.1281523
## 
## $lnL
## [1] -77.1751
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 160.3502
## 
## $aicc
## [1] 160.8502

AIC

aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
                   c("BM","OU","EB"))
aic.vals
##       BM       OU       EB 
## 158.5947 144.0077 160.8502

weighted AIC

aic.w(aic.vals)
##         BM         OU         EB 
## 0.00067931 0.99910075 0.00021994


ePLA2

dat<-setNames(trait$ePLA2,rownames(trait))

fitBM<-fitContinuous(tree,dat)
fitOU<-fitContinuous(tree,dat,model="OU")
fitEB<-fitContinuous(tree,dat,model="EB")

BM model

fitBM$opt
## $sigsq
## [1] 0.01783931
## 
## $z0
## [1] 0.00254227
## 
## $lnL
## [1] -51.36715
## 
## $method
## [1] "Brent"
## 
## $k
## [1] 2
## 
## $aic
## [1] 106.7343
## 
## $aicc
## [1] 106.9792

OU model

fitOU$opt
## $alpha
## [1] 0.003905488
## 
## $sigsq
## [1] 0.01966365
## 
## $z0
## [1] 0.01119636
## 
## $lnL
## [1] -51.3004
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 108.6008
## 
## $aicc
## [1] 109.1008

EB model

fitEB$opt
## $a
## [1] -1e-06
## 
## $sigsq
## [1] 0.01784019
## 
## $z0
## [1] 0.002541179
## 
## $lnL
## [1] -51.36717
## 
## $method
## [1] "L-BFGS-B"
## 
## $k
## [1] 3
## 
## $aic
## [1] 108.7343
## 
## $aicc
## [1] 109.2343

AIC

aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
                   c("BM","OU","EB"))
aic.vals
##       BM       OU       EB 
## 106.9792 109.1008 109.2343

weighted AIC

aic.w(aic.vals)
##        BM        OU        EB 
## 0.5988027 0.2072932 0.1939041

Testing multi Optioma OU models with OUwie

Regime classification:1

tree<-read.nexus("./data/Final_tree.nex")
dat<-read.csv("./data/Ouwie_data/BPP_OUwie_ManyOptions_optima.csv",row.names = 1)

Make simmap tree for selective regime. We classified selective regime based on the phylomorphospace obtained from Barua and Mikheyev 2019. Figure below shows which snakes were clustered into which regime.

ad_reg<-setNames(dat[,2],rownames(dat))
simmap.tre<-make.simmap(tree, ad_reg, model = "ER")
## make.simmap is sampling character histories conditioned on the transition matrix
## 
## Q =
##              1            2            3            4            5
## 1 -0.015510466  0.002585078  0.002585078  0.002585078  0.002585078
## 2  0.002585078 -0.015510466  0.002585078  0.002585078  0.002585078
## 3  0.002585078  0.002585078 -0.015510466  0.002585078  0.002585078
## 4  0.002585078  0.002585078  0.002585078 -0.015510466  0.002585078
## 5  0.002585078  0.002585078  0.002585078  0.002585078 -0.015510466
## 6  0.002585078  0.002585078  0.002585078  0.002585078  0.002585078
## 7  0.002585078  0.002585078  0.002585078  0.002585078  0.002585078
##              6            7
## 1  0.002585078  0.002585078
## 2  0.002585078  0.002585078
## 3  0.002585078  0.002585078
## 4  0.002585078  0.002585078
## 5  0.002585078  0.002585078
## 6 -0.015510466  0.002585078
## 7  0.002585078 -0.015510466
## (estimated using likelihood);
## and (mean) root node prior probabilities
## pi =
##         1         2         3         4         5         6         7 
## 0.1428571 0.1428571 0.1428571 0.1428571 0.1428571 0.1428571 0.1428571
## Done.
plot(simmap.tre,type="fan",fsize=0.5,ftype="i")
## no colors provided. using the following legend:
##         1         2         3         4         5         6         7 
##   "black"     "red"  "green3"    "blue"    "cyan" "magenta"  "yellow"

SVSP

dat<-read.csv("./data/Ouwie_data/SVSP_OUwie_ManyOptions_optima.csv")

BM

BM1_SVSP<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
BM1_SVSP
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 158.2624 158.5073 162.1649   BM1   52
## 
## Rates
##          -0.028433826 -0.065786707 -0.065788923 -0.091682733 -0.196308172
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.254442424 -0.259222055 -0.26328121 -0.272798588 -0.284773794
## alpha              NA           NA          NA           NA           NA
## sigma.sq   0.04805937   0.04805937  0.04805937   0.04805937   0.04805937
##          -0.323558544 -0.327981232 -0.335892953 -0.351479006 -0.359161832
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.380235729 -0.399213836 -0.399284019 -0.4527582 -0.453846945
## alpha              NA           NA           NA         NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937 0.04805937   0.04805937
##          -0.454790159 -0.463327573 -0.463654083 -0.473209269 -0.478528704
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.478787643 -0.505966472 -0.576323477 -0.599651816 -0.612242656
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.699934584 0.02381373 0.063071096 0.068901152 0.093272473
## alpha              NA         NA          NA          NA          NA
## sigma.sq   0.04805937 0.04805937  0.04805937  0.04805937  0.04805937
##          0.095307031 0.222783197 0.297477307 0.378206741 0.549678091
## alpha             NA          NA          NA          NA          NA
## sigma.sq  0.04805937  0.04805937  0.04805937  0.04805937  0.04805937
##          1.11791987 1.13186312 1.174566834 1.199064792 1.301684098
## alpha            NA         NA          NA          NA          NA
## sigma.sq 0.04805937 0.04805937  0.04805937  0.04805937  0.04805937
##          1.30629117 1.79412254 2.149960947 2.268008945 2.538965324
## alpha            NA         NA          NA          NA          NA
## sigma.sq 0.04805937 0.04805937  0.04805937  0.04805937  0.04805937
##          2.604500193 2.842844084  inode3122  inode3123  inode3151
## alpha             NA          NA         NA         NA         NA
## sigma.sq  0.04805937  0.04805937 0.04805937 0.04805937 0.04805937
##           inode3159  inode3160  inode3162  inode3217  inode3218  inode3219
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3238  inode3239  inode3241  inode3242  inode3246  inode3259
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3264  inode3269  inode3272  inode3274  inode3279  inode3280
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3282  inode3284  inode3288  inode3290  inode3297  inode3301
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3315  inode3316  inode3319  inode3326  inode3351  inode3490
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3495  inode3496  inode3501  inode3502  inode3509  inode3513
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3514  inode3525  inode3538  inode3542  inode3572  inode3631
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3714  inode3732  inode3769  inode3970  inode4032  inode4086
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 
## Optima
##          -0.028433826 -0.065786707 -0.065788923 -0.091682733 -0.196308172
## estimate    4.0576335            0            0            0            0
## se          0.7261147            0            0            0            0
##          -0.254442424 -0.259222055 -0.26328121 -0.272798588 -0.284773794
## estimate            0            0           0            0            0
## se                  0            0           0            0            0
##          -0.323558544 -0.327981232 -0.335892953 -0.351479006 -0.359161832
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.380235729 -0.399213836 -0.399284019 -0.4527582 -0.453846945
## estimate            0            0            0          0            0
## se                  0            0            0          0            0
##          -0.454790159 -0.463327573 -0.463654083 -0.473209269 -0.478528704
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.478787643 -0.505966472 -0.576323477 -0.599651816 -0.612242656
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.699934584 0.02381373 0.063071096 0.068901152 0.093272473
## estimate            0          0           0           0           0
## se                  0          0           0           0           0
##          0.095307031 0.222783197 0.297477307 0.378206741 0.549678091
## estimate           0           0           0           0           0
## se                 0           0           0           0           0
##          1.11791987 1.13186312 1.174566834 1.199064792 1.301684098
## estimate          0          0           0           0           0
## se                0          0           0           0           0
##          1.30629117 1.79412254 2.149960947 2.268008945 2.538965324
## estimate          0          0           0           0           0
## se                0          0           0           0           0
##          2.604500193 2.842844084 inode3122 inode3123 inode3151 inode3159
## estimate           0           0         0         0         0         0
## se                 0           0         0         0         0         0
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate         0         0         0         0         0
## se               0         0         0         0         0
## 
## Arrived at a reliable solution

OU1

OU1_SVSP<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OU1_SVSP
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 160.2624 160.7624 166.1161   OU1   52
## 
## Rates
##          -0.028433826 -0.065786707 -0.065788923 -0.091682733 -0.196308172
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.254442424 -0.259222055  -0.26328121 -0.272798588 -0.284773794
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.323558544 -0.327981232 -0.335892953 -0.351479006 -0.359161832
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.380235729 -0.399213836 -0.399284019   -0.4527582 -0.453846945
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.454790159 -0.463327573 -0.463654083 -0.473209269 -0.478528704
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.478787643 -0.505966472 -0.576323477 -0.599651816 -0.612242656
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.699934584   0.02381373  0.063071096  0.068901152  0.093272473
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           0.095307031  0.222783197  0.297477307  0.378206741  0.549678091
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##            1.11791987   1.13186312  1.174566834  1.199064792  1.301684098
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##            1.30629117   1.79412254  2.149960947  2.268008945  2.538965324
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           2.604500193  2.842844084    inode3122    inode3123    inode3151
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3159    inode3160    inode3162    inode3217    inode3218
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3219    inode3238    inode3239    inode3241    inode3242
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3246    inode3259    inode3264    inode3269    inode3272
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3274    inode3279    inode3280    inode3282    inode3284
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3288    inode3290    inode3297    inode3301    inode3315
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3316    inode3319    inode3326    inode3351    inode3490
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3495    inode3496    inode3501    inode3502    inode3509
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3513    inode3514    inode3525    inode3538    inode3542
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3572    inode3631    inode3714    inode3732    inode3769
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3970    inode4032    inode4086
## alpha    2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
## 
## 
## Optima
##          -0.028433826 -0.065786707 -0.065788923 -0.091682733 -0.196308172
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.254442424 -0.259222055 -0.26328121 -0.272798588 -0.284773794
## estimate    4.0576335    4.0576335   4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536   0.7260536    0.7260536    0.7260536
##          -0.323558544 -0.327981232 -0.335892953 -0.351479006 -0.359161832
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.380235729 -0.399213836 -0.399284019 -0.4527582 -0.453846945
## estimate    4.0576335    4.0576335    4.0576335  4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536  0.7260536    0.7260536
##          -0.454790159 -0.463327573 -0.463654083 -0.473209269 -0.478528704
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.478787643 -0.505966472 -0.576323477 -0.599651816 -0.612242656
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.699934584 0.02381373 0.063071096 0.068901152 0.093272473
## estimate    4.0576335  4.0576335   4.0576335   4.0576335   4.0576335
## se          0.7260536  0.7260536   0.7260536   0.7260536   0.7260536
##          0.095307031 0.222783197 0.297477307 0.378206741 0.549678091
## estimate   4.0576335   4.0576335   4.0576335   4.0576335   4.0576335
## se         0.7260536   0.7260536   0.7260536   0.7260536   0.7260536
##          1.11791987 1.13186312 1.174566834 1.199064792 1.301684098
## estimate  4.0576335  4.0576335   4.0576335   4.0576335   4.0576335
## se        0.7260536  0.7260536   0.7260536   0.7260536   0.7260536
##          1.30629117 1.79412254 2.149960947 2.268008945 2.538965324
## estimate  4.0576335  4.0576335   4.0576335   4.0576335   4.0576335
## se        0.7260536  0.7260536   0.7260536   0.7260536   0.7260536
##          2.604500193 2.842844084 inode3122 inode3123 inode3151 inode3159
## estimate   4.0576335   4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se         0.7260536   0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 
## 
## Half life (another way of reporting alpha)
## -0.028433826 -0.065786707 -0.065788923 -0.091682733 -0.196308172 
##    308643937    308643937    308643937    308643937    308643937 
## -0.254442424 -0.259222055  -0.26328121 -0.272798588 -0.284773794 
##    308643937    308643937    308643937    308643937    308643937 
## -0.323558544 -0.327981232 -0.335892953 -0.351479006 -0.359161832 
##    308643937    308643937    308643937    308643937    308643937 
## -0.380235729 -0.399213836 -0.399284019   -0.4527582 -0.453846945 
##    308643937    308643937    308643937    308643937    308643937 
## -0.454790159 -0.463327573 -0.463654083 -0.473209269 -0.478528704 
##    308643937    308643937    308643937    308643937    308643937 
## -0.478787643 -0.505966472 -0.576323477 -0.599651816 -0.612242656 
##    308643937    308643937    308643937    308643937    308643937 
## -0.699934584   0.02381373  0.063071096  0.068901152  0.093272473 
##    308643937    308643937    308643937    308643937    308643937 
##  0.095307031  0.222783197  0.297477307  0.378206741  0.549678091 
##    308643937    308643937    308643937    308643937    308643937 
##   1.11791987   1.13186312  1.174566834  1.199064792  1.301684098 
##    308643937    308643937    308643937    308643937    308643937 
##   1.30629117   1.79412254  2.149960947  2.268008945  2.538965324 
##    308643937    308643937    308643937    308643937    308643937 
##  2.604500193  2.842844084    inode3122    inode3123    inode3151 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3159    inode3160    inode3162    inode3217    inode3218 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3219    inode3238    inode3239    inode3241    inode3242 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3246    inode3259    inode3264    inode3269    inode3272 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3274    inode3279    inode3280    inode3282    inode3284 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3288    inode3290    inode3297    inode3301    inode3315 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3316    inode3319    inode3326    inode3351    inode3490 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3495    inode3496    inode3501    inode3502    inode3509 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3513    inode3514    inode3525    inode3538    inode3542 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3572    inode3631    inode3714    inode3732    inode3769 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3970    inode4032    inode4086 
##    308643937    308643937    308643937 
## 
## Arrived at a reliable solution
OU1_SVSP$eigval
## [1] 2.6e+01 1.3e-06
OU1_SVSP$solution.se
##          -0.028433826 -0.065786707 -0.065788923 -0.091682733 -0.196308172
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.254442424 -0.259222055 -0.26328121 -0.272798588 -0.284773794
## alpha     882.7127566  882.7127566 882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103   0.1961103    0.1961103    0.1961103
##          -0.323558544 -0.327981232 -0.335892953 -0.351479006 -0.359161832
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.380235729 -0.399213836 -0.399284019  -0.4527582 -0.453846945
## alpha     882.7127566  882.7127566  882.7127566 882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103   0.1961103    0.1961103
##          -0.454790159 -0.463327573 -0.463654083 -0.473209269 -0.478528704
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.478787643 -0.505966472 -0.576323477 -0.599651816 -0.612242656
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.699934584  0.02381373 0.063071096 0.068901152 0.093272473
## alpha     882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq    0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##          0.095307031 0.222783197 0.297477307 0.378206741 0.549678091
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##           1.11791987  1.13186312 1.174566834 1.199064792 1.301684098
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##           1.30629117  1.79412254 2.149960947 2.268008945 2.538965324
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##          2.604500193 2.842844084   inode3122   inode3123   inode3151
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3159   inode3160   inode3162   inode3217   inode3218
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3219   inode3238   inode3239   inode3241   inode3242
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3246   inode3259   inode3264   inode3269   inode3272
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3274   inode3279   inode3280   inode3282   inode3284
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3288   inode3290   inode3297   inode3301   inode3315
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3316   inode3319   inode3326   inode3351   inode3490
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3495   inode3496   inode3501   inode3502   inode3509
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3513   inode3514   inode3525   inode3538   inode3542
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3572   inode3631   inode3714   inode3732   inode3769
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3970   inode4032   inode4086
## alpha    882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103

OUM

OUM_SVSP<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OUM_SVSP
## 
## Fit
##       lnL       AIC     AICc       BIC model ntax
##  85.24088 -152.4818 -148.196 -134.9206   OUM   52
## 
## 
## Rates
##                   1          2          3          4          5          6
## alpha    5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
##                   7
## alpha    5.78373949
## sigma.sq 0.02552326
## 
## Optima
##                   1          2          3          4          5          6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se       0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
##                   7
## estimate 6.99998674
## se       0.01485411
## 
## 
## Half life (another way of reporting alpha)
##         1         2         3         4         5         6         7 
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 
## 
## Arrived at a reliable solution

AIC

aic<-setNames(c(BM1_SVSP$AICc,OU1_SVSP$AICc,OUM_SVSP$AICc),
              c("BM","OU1","OUM"))
aic
##        BM       OU1       OUM 
##  158.5073  160.7624 -148.1960
aic.w(aic)
##  BM OU1 OUM 
##   0   0   1

TFTx

dat<-read.csv("./data/Ouwie_data/TFTx_OUwie_ManyOptions_optima.csv")

BM

BM1_TFTx<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
BM1_TFTx
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 158.2624 158.5073 162.1649   BM1   52
## 
## Rates
##          -0.140629497 -0.151281523 -0.339477428 -0.343935613 -0.351900922
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.363737891 -0.36429282 -0.421421201 -0.428224485 -0.449261397
## alpha              NA          NA           NA           NA           NA
## sigma.sq   0.04805937  0.04805937   0.04805937   0.04805937   0.04805937
##          -0.460376482 -0.466734078 -0.467614451 -0.471887205 -0.473776068
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.478411682 -0.481264314 -0.492629779 -0.494906486 -0.52278517
## alpha              NA           NA           NA           NA          NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937  0.04805937
##          -0.523308863 -0.535408592 -0.539435104 -0.542252225 -0.543732229
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.555961591 -0.569277353 -0.581015956 -0.589669336 -0.632877207
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.657107195 -0.665162495 -0.709372748 -0.731309262 -0.827893652
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.96572225 0.73567568 0.739710541 1.123078765 1.340010728
## alpha             NA         NA          NA          NA          NA
## sigma.sq  0.04805937 0.04805937  0.04805937  0.04805937  0.04805937
##          1.804132426 2.419250025 2.421919481 2.58619344 2.662975226
## alpha             NA          NA          NA         NA          NA
## sigma.sq  0.04805937  0.04805937  0.04805937 0.04805937  0.04805937
##          2.722817222 2.742528187 2.750632477 2.807834797 2.839970361
## alpha             NA          NA          NA          NA          NA
## sigma.sq  0.04805937  0.04805937  0.04805937  0.04805937  0.04805937
##          2.844393257 2.845816956  inode3122  inode3123  inode3151
## alpha             NA          NA         NA         NA         NA
## sigma.sq  0.04805937  0.04805937 0.04805937 0.04805937 0.04805937
##           inode3159  inode3160  inode3162  inode3217  inode3218  inode3219
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3238  inode3239  inode3241  inode3242  inode3246  inode3259
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3264  inode3269  inode3272  inode3274  inode3279  inode3280
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3282  inode3284  inode3288  inode3290  inode3297  inode3301
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3315  inode3316  inode3319  inode3326  inode3351  inode3490
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3495  inode3496  inode3501  inode3502  inode3509  inode3513
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3514  inode3525  inode3538  inode3542  inode3572  inode3631
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3714  inode3732  inode3769  inode3970  inode4032  inode4086
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 
## Optima
##          -0.140629497 -0.151281523 -0.339477428 -0.343935613 -0.351900922
## estimate    4.0576335            0            0            0            0
## se          0.7261147            0            0            0            0
##          -0.363737891 -0.36429282 -0.421421201 -0.428224485 -0.449261397
## estimate            0           0            0            0            0
## se                  0           0            0            0            0
##          -0.460376482 -0.466734078 -0.467614451 -0.471887205 -0.473776068
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.478411682 -0.481264314 -0.492629779 -0.494906486 -0.52278517
## estimate            0            0            0            0           0
## se                  0            0            0            0           0
##          -0.523308863 -0.535408592 -0.539435104 -0.542252225 -0.543732229
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.555961591 -0.569277353 -0.581015956 -0.589669336 -0.632877207
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.657107195 -0.665162495 -0.709372748 -0.731309262 -0.827893652
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.96572225 0.73567568 0.739710541 1.123078765 1.340010728
## estimate           0          0           0           0           0
## se                 0          0           0           0           0
##          1.804132426 2.419250025 2.421919481 2.58619344 2.662975226
## estimate           0           0           0          0           0
## se                 0           0           0          0           0
##          2.722817222 2.742528187 2.750632477 2.807834797 2.839970361
## estimate           0           0           0           0           0
## se                 0           0           0           0           0
##          2.844393257 2.845816956 inode3122 inode3123 inode3151 inode3159
## estimate           0           0         0         0         0         0
## se                 0           0         0         0         0         0
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate         0         0         0         0         0
## se               0         0         0         0         0
## 
## Arrived at a reliable solution

OU1

OU1_TFTx<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OU1_TFTx
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 160.2624 160.7624 166.1161   OU1   52
## 
## Rates
##          -0.140629497 -0.151281523 -0.339477428 -0.343935613 -0.351900922
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.363737891  -0.36429282 -0.421421201 -0.428224485 -0.449261397
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.460376482 -0.466734078 -0.467614451 -0.471887205 -0.473776068
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.478411682 -0.481264314 -0.492629779 -0.494906486  -0.52278517
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.523308863 -0.535408592 -0.539435104 -0.542252225 -0.543732229
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.555961591 -0.569277353 -0.581015956 -0.589669336 -0.632877207
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.657107195 -0.665162495 -0.709372748 -0.731309262 -0.827893652
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           -0.96572225   0.73567568  0.739710541  1.123078765  1.340010728
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           1.804132426  2.419250025  2.421919481   2.58619344  2.662975226
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           2.722817222  2.742528187  2.750632477  2.807834797  2.839970361
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           2.844393257  2.845816956    inode3122    inode3123    inode3151
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3159    inode3160    inode3162    inode3217    inode3218
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3219    inode3238    inode3239    inode3241    inode3242
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3246    inode3259    inode3264    inode3269    inode3272
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3274    inode3279    inode3280    inode3282    inode3284
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3288    inode3290    inode3297    inode3301    inode3315
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3316    inode3319    inode3326    inode3351    inode3490
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3495    inode3496    inode3501    inode3502    inode3509
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3513    inode3514    inode3525    inode3538    inode3542
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3572    inode3631    inode3714    inode3732    inode3769
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3970    inode4032    inode4086
## alpha    2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
## 
## 
## Optima
##          -0.140629497 -0.151281523 -0.339477428 -0.343935613 -0.351900922
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.363737891 -0.36429282 -0.421421201 -0.428224485 -0.449261397
## estimate    4.0576335   4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536   0.7260536    0.7260536    0.7260536    0.7260536
##          -0.460376482 -0.466734078 -0.467614451 -0.471887205 -0.473776068
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.478411682 -0.481264314 -0.492629779 -0.494906486 -0.52278517
## estimate    4.0576335    4.0576335    4.0576335    4.0576335   4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536   0.7260536
##          -0.523308863 -0.535408592 -0.539435104 -0.542252225 -0.543732229
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.555961591 -0.569277353 -0.581015956 -0.589669336 -0.632877207
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.657107195 -0.665162495 -0.709372748 -0.731309262 -0.827893652
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.96572225 0.73567568 0.739710541 1.123078765 1.340010728
## estimate   4.0576335  4.0576335   4.0576335   4.0576335   4.0576335
## se         0.7260536  0.7260536   0.7260536   0.7260536   0.7260536
##          1.804132426 2.419250025 2.421919481 2.58619344 2.662975226
## estimate   4.0576335   4.0576335   4.0576335  4.0576335   4.0576335
## se         0.7260536   0.7260536   0.7260536  0.7260536   0.7260536
##          2.722817222 2.742528187 2.750632477 2.807834797 2.839970361
## estimate   4.0576335   4.0576335   4.0576335   4.0576335   4.0576335
## se         0.7260536   0.7260536   0.7260536   0.7260536   0.7260536
##          2.844393257 2.845816956 inode3122 inode3123 inode3151 inode3159
## estimate   4.0576335   4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se         0.7260536   0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 
## 
## Half life (another way of reporting alpha)
## -0.140629497 -0.151281523 -0.339477428 -0.343935613 -0.351900922 
##    308643937    308643937    308643937    308643937    308643937 
## -0.363737891  -0.36429282 -0.421421201 -0.428224485 -0.449261397 
##    308643937    308643937    308643937    308643937    308643937 
## -0.460376482 -0.466734078 -0.467614451 -0.471887205 -0.473776068 
##    308643937    308643937    308643937    308643937    308643937 
## -0.478411682 -0.481264314 -0.492629779 -0.494906486  -0.52278517 
##    308643937    308643937    308643937    308643937    308643937 
## -0.523308863 -0.535408592 -0.539435104 -0.542252225 -0.543732229 
##    308643937    308643937    308643937    308643937    308643937 
## -0.555961591 -0.569277353 -0.581015956 -0.589669336 -0.632877207 
##    308643937    308643937    308643937    308643937    308643937 
## -0.657107195 -0.665162495 -0.709372748 -0.731309262 -0.827893652 
##    308643937    308643937    308643937    308643937    308643937 
##  -0.96572225   0.73567568  0.739710541  1.123078765  1.340010728 
##    308643937    308643937    308643937    308643937    308643937 
##  1.804132426  2.419250025  2.421919481   2.58619344  2.662975226 
##    308643937    308643937    308643937    308643937    308643937 
##  2.722817222  2.742528187  2.750632477  2.807834797  2.839970361 
##    308643937    308643937    308643937    308643937    308643937 
##  2.844393257  2.845816956    inode3122    inode3123    inode3151 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3159    inode3160    inode3162    inode3217    inode3218 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3219    inode3238    inode3239    inode3241    inode3242 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3246    inode3259    inode3264    inode3269    inode3272 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3274    inode3279    inode3280    inode3282    inode3284 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3288    inode3290    inode3297    inode3301    inode3315 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3316    inode3319    inode3326    inode3351    inode3490 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3495    inode3496    inode3501    inode3502    inode3509 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3513    inode3514    inode3525    inode3538    inode3542 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3572    inode3631    inode3714    inode3732    inode3769 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3970    inode4032    inode4086 
##    308643937    308643937    308643937 
## 
## Arrived at a reliable solution
OU1_TFTx$eigval
## [1] 2.6e+01 1.3e-06
OU1_TFTx$solution.se
##          -0.140629497 -0.151281523 -0.339477428 -0.343935613 -0.351900922
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.363737891 -0.36429282 -0.421421201 -0.428224485 -0.449261397
## alpha     882.7127566 882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103   0.1961103    0.1961103    0.1961103    0.1961103
##          -0.460376482 -0.466734078 -0.467614451 -0.471887205 -0.473776068
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.478411682 -0.481264314 -0.492629779 -0.494906486 -0.52278517
## alpha     882.7127566  882.7127566  882.7127566  882.7127566 882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103   0.1961103
##          -0.523308863 -0.535408592 -0.539435104 -0.542252225 -0.543732229
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.555961591 -0.569277353 -0.581015956 -0.589669336 -0.632877207
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.657107195 -0.665162495 -0.709372748 -0.731309262 -0.827893652
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.96572225  0.73567568 0.739710541 1.123078765 1.340010728
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##          1.804132426 2.419250025 2.421919481  2.58619344 2.662975226
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##          2.722817222 2.742528187 2.750632477 2.807834797 2.839970361
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##          2.844393257 2.845816956   inode3122   inode3123   inode3151
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3159   inode3160   inode3162   inode3217   inode3218
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3219   inode3238   inode3239   inode3241   inode3242
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3246   inode3259   inode3264   inode3269   inode3272
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3274   inode3279   inode3280   inode3282   inode3284
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3288   inode3290   inode3297   inode3301   inode3315
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3316   inode3319   inode3326   inode3351   inode3490
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3495   inode3496   inode3501   inode3502   inode3509
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3513   inode3514   inode3525   inode3538   inode3542
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3572   inode3631   inode3714   inode3732   inode3769
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3970   inode4032   inode4086
## alpha    882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103

OUM

OUM_TFTx<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OUM_TFTx
## 
## Fit
##       lnL       AIC     AICc       BIC model ntax
##  85.24088 -152.4818 -148.196 -134.9206   OUM   52
## 
## 
## Rates
##                   1          2          3          4          5          6
## alpha    5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
##                   7
## alpha    5.78373949
## sigma.sq 0.02552326
## 
## Optima
##                   1          2          3          4          5          6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se       0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
##                   7
## estimate 6.99998674
## se       0.01485411
## 
## 
## Half life (another way of reporting alpha)
##         1         2         3         4         5         6         7 
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 
## 
## Arrived at a reliable solution

AIC

aic<-setNames(c(BM1_TFTx$AICc,OU1_TFTx$AICc,OUM_TFTx$AICc),
              c("BM","OU1","OUM"))
aic
##        BM       OU1       OUM 
##  158.5073  160.7624 -148.1960
aic.w(aic)
##  BM OU1 OUM 
##   0   0   1

SVMP

dat<-read.csv("./data/Ouwie_data/SVMP_OUwie_ManyOptions_optima.csv")

BM

BM1_SVMP<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
BM1_SVMP
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -93.44696 190.8939 191.1388 194.7964   BM1   52
## 
## Rates
##          -0.028600184 -0.160843603 -0.235324367 -0.314729465 -0.331612132
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.09001418   0.09001418   0.09001418   0.09001418   0.09001418
##          -0.334277933 -0.336945636 -0.337468929 -0.399213836 -0.399284019
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.09001418   0.09001418   0.09001418   0.09001418   0.09001418
##          -0.4034999 -0.454790159 -0.483120435 -0.498780177 -0.508750647
## alpha            NA           NA           NA           NA           NA
## sigma.sq 0.09001418   0.09001418   0.09001418   0.09001418   0.09001418
##          -0.556403047 -0.563339519 -0.612242656 0.24612442 0.688226777
## alpha              NA           NA           NA         NA          NA
## sigma.sq   0.09001418   0.09001418   0.09001418 0.09001418  0.09001418
##          0.716248171 0.800457806 0.852053529 0.884429117 1.105054626
## alpha             NA          NA          NA          NA          NA
## sigma.sq  0.09001418  0.09001418  0.09001418  0.09001418  0.09001418
##          1.501471811 1.730054146 1.739986761 1.938191918 2.055614142
## alpha             NA          NA          NA          NA          NA
## sigma.sq  0.09001418  0.09001418  0.09001418  0.09001418  0.09001418
##          2.13114086 2.347170187 2.350545516 2.38904884 2.485664868
## alpha            NA          NA          NA         NA          NA
## sigma.sq 0.09001418  0.09001418  0.09001418 0.09001418  0.09001418
##          2.505774697 2.566762637 2.574411326 2.706669156 2.712007513
## alpha             NA          NA          NA          NA          NA
## sigma.sq  0.09001418  0.09001418  0.09001418  0.09001418  0.09001418
##          2.722965014 2.732313956 2.73286191 2.751484952 2.753080674
## alpha             NA          NA         NA          NA          NA
## sigma.sq  0.09001418  0.09001418 0.09001418  0.09001418  0.09001418
##          2.760067398 2.774368128 2.795360528 2.803163813 2.806058383
## alpha             NA          NA          NA          NA          NA
## sigma.sq  0.09001418  0.09001418  0.09001418  0.09001418  0.09001418
##          2.821722852 2.840055323  inode3122  inode3123  inode3151
## alpha             NA          NA         NA         NA         NA
## sigma.sq  0.09001418  0.09001418 0.09001418 0.09001418 0.09001418
##           inode3159  inode3160  inode3162  inode3217  inode3218  inode3219
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
##           inode3238  inode3239  inode3241  inode3242  inode3246  inode3259
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
##           inode3264  inode3269  inode3272  inode3274  inode3279  inode3280
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
##           inode3282  inode3284  inode3288  inode3290  inode3297  inode3301
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
##           inode3315  inode3316  inode3319  inode3326  inode3351  inode3490
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
##           inode3495  inode3496  inode3501  inode3502  inode3509  inode3513
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
##           inode3514  inode3525  inode3538  inode3542  inode3572  inode3631
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
##           inode3714  inode3732  inode3769  inode3970  inode4032  inode4086
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## 
## Optima
##          -0.028600184 -0.160843603 -0.235324367 -0.314729465 -0.331612132
## estimate    2.3849719            0            0            0            0
## se          0.9937374            0            0            0            0
##          -0.334277933 -0.336945636 -0.337468929 -0.399213836 -0.399284019
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.4034999 -0.454790159 -0.483120435 -0.498780177 -0.508750647
## estimate          0            0            0            0            0
## se                0            0            0            0            0
##          -0.556403047 -0.563339519 -0.612242656 0.24612442 0.688226777
## estimate            0            0            0          0           0
## se                  0            0            0          0           0
##          0.716248171 0.800457806 0.852053529 0.884429117 1.105054626
## estimate           0           0           0           0           0
## se                 0           0           0           0           0
##          1.501471811 1.730054146 1.739986761 1.938191918 2.055614142
## estimate           0           0           0           0           0
## se                 0           0           0           0           0
##          2.13114086 2.347170187 2.350545516 2.38904884 2.485664868
## estimate          0           0           0          0           0
## se                0           0           0          0           0
##          2.505774697 2.566762637 2.574411326 2.706669156 2.712007513
## estimate           0           0           0           0           0
## se                 0           0           0           0           0
##          2.722965014 2.732313956 2.73286191 2.751484952 2.753080674
## estimate           0           0          0           0           0
## se                 0           0          0           0           0
##          2.760067398 2.774368128 2.795360528 2.803163813 2.806058383
## estimate           0           0           0           0           0
## se                 0           0           0           0           0
##          2.821722852 2.840055323 inode3122 inode3123 inode3151 inode3159
## estimate           0           0         0         0         0         0
## se                 0           0         0         0         0         0
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate         0         0         0         0         0
## se               0         0         0         0         0
## 
## Arrived at a reliable solution

OU1

OU1_SVMP<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
## Warning in sqrt(diag(pseudoinverse(h))): NaNs produced
OU1_SVMP
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -93.44696 192.8939 193.3939 198.7477   OU1   52
## 
## Rates
##          -0.028600184 -0.160843603 -0.235324367 -0.314729465 -0.331612132
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##          -0.334277933 -0.336945636 -0.337468929 -0.399213836 -0.399284019
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##            -0.4034999 -0.454790159 -0.483120435 -0.498780177 -0.508750647
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##          -0.556403047 -0.563339519 -0.612242656   0.24612442  0.688226777
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##           0.716248171  0.800457806  0.852053529  0.884429117  1.105054626
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##           1.501471811  1.730054146  1.739986761  1.938191918  2.055614142
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##            2.13114086  2.347170187  2.350545516   2.38904884  2.485664868
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##           2.505774697  2.566762637  2.574411326  2.706669156  2.712007513
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##           2.722965014  2.732313956   2.73286191  2.751484952  2.753080674
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##           2.760067398  2.774368128  2.795360528  2.803163813  2.806058383
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##           2.821722852  2.840055323    inode3122    inode3123    inode3151
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##             inode3159    inode3160    inode3162    inode3217    inode3218
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##             inode3219    inode3238    inode3239    inode3241    inode3242
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##             inode3246    inode3259    inode3264    inode3269    inode3272
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##             inode3274    inode3279    inode3280    inode3282    inode3284
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##             inode3288    inode3290    inode3297    inode3301    inode3315
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##             inode3316    inode3319    inode3326    inode3351    inode3490
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##             inode3495    inode3496    inode3501    inode3502    inode3509
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##             inode3513    inode3514    inode3525    inode3538    inode3542
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##             inode3572    inode3631    inode3714    inode3732    inode3769
## alpha    2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
##             inode3970    inode4032    inode4086
## alpha    2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02
## 
## 
## Optima
##          -0.028600184 -0.160843603 -0.235324367 -0.314729465 -0.331612132
## estimate    2.3849719    2.3849719    2.3849719    2.3849719    2.3849719
## se          0.9936895    0.9936895    0.9936895    0.9936895    0.9936895
##          -0.334277933 -0.336945636 -0.337468929 -0.399213836 -0.399284019
## estimate    2.3849719    2.3849719    2.3849719    2.3849719    2.3849719
## se          0.9936895    0.9936895    0.9936895    0.9936895    0.9936895
##          -0.4034999 -0.454790159 -0.483120435 -0.498780177 -0.508750647
## estimate  2.3849719    2.3849719    2.3849719    2.3849719    2.3849719
## se        0.9936895    0.9936895    0.9936895    0.9936895    0.9936895
##          -0.556403047 -0.563339519 -0.612242656 0.24612442 0.688226777
## estimate    2.3849719    2.3849719    2.3849719  2.3849719   2.3849719
## se          0.9936895    0.9936895    0.9936895  0.9936895   0.9936895
##          0.716248171 0.800457806 0.852053529 0.884429117 1.105054626
## estimate   2.3849719   2.3849719   2.3849719   2.3849719   2.3849719
## se         0.9936895   0.9936895   0.9936895   0.9936895   0.9936895
##          1.501471811 1.730054146 1.739986761 1.938191918 2.055614142
## estimate   2.3849719   2.3849719   2.3849719   2.3849719   2.3849719
## se         0.9936895   0.9936895   0.9936895   0.9936895   0.9936895
##          2.13114086 2.347170187 2.350545516 2.38904884 2.485664868
## estimate  2.3849719   2.3849719   2.3849719  2.3849719   2.3849719
## se        0.9936895   0.9936895   0.9936895  0.9936895   0.9936895
##          2.505774697 2.566762637 2.574411326 2.706669156 2.712007513
## estimate   2.3849719   2.3849719   2.3849719   2.3849719   2.3849719
## se         0.9936895   0.9936895   0.9936895   0.9936895   0.9936895
##          2.722965014 2.732313956 2.73286191 2.751484952 2.753080674
## estimate   2.3849719   2.3849719  2.3849719   2.3849719   2.3849719
## se         0.9936895   0.9936895  0.9936895   0.9936895   0.9936895
##          2.760067398 2.774368128 2.795360528 2.803163813 2.806058383
## estimate   2.3849719   2.3849719   2.3849719   2.3849719   2.3849719
## se         0.9936895   0.9936895   0.9936895   0.9936895   0.9936895
##          2.821722852 2.840055323 inode3122 inode3123 inode3151 inode3159
## estimate   2.3849719   2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se         0.9936895   0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se       0.9936895 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se       0.9936895 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se       0.9936895 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se       0.9936895 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se       0.9936895 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se       0.9936895 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se       0.9936895 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se       0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## 
## 
## Half life (another way of reporting alpha)
## -0.028600184 -0.160843603 -0.235324367 -0.314729465 -0.331612132 
##    336290887    336290887    336290887    336290887    336290887 
## -0.334277933 -0.336945636 -0.337468929 -0.399213836 -0.399284019 
##    336290887    336290887    336290887    336290887    336290887 
##   -0.4034999 -0.454790159 -0.483120435 -0.498780177 -0.508750647 
##    336290887    336290887    336290887    336290887    336290887 
## -0.556403047 -0.563339519 -0.612242656   0.24612442  0.688226777 
##    336290887    336290887    336290887    336290887    336290887 
##  0.716248171  0.800457806  0.852053529  0.884429117  1.105054626 
##    336290887    336290887    336290887    336290887    336290887 
##  1.501471811  1.730054146  1.739986761  1.938191918  2.055614142 
##    336290887    336290887    336290887    336290887    336290887 
##   2.13114086  2.347170187  2.350545516   2.38904884  2.485664868 
##    336290887    336290887    336290887    336290887    336290887 
##  2.505774697  2.566762637  2.574411326  2.706669156  2.712007513 
##    336290887    336290887    336290887    336290887    336290887 
##  2.722965014  2.732313956   2.73286191  2.751484952  2.753080674 
##    336290887    336290887    336290887    336290887    336290887 
##  2.760067398  2.774368128  2.795360528  2.803163813  2.806058383 
##    336290887    336290887    336290887    336290887    336290887 
##  2.821722852  2.840055323    inode3122    inode3123    inode3151 
##    336290887    336290887    336290887    336290887    336290887 
##    inode3159    inode3160    inode3162    inode3217    inode3218 
##    336290887    336290887    336290887    336290887    336290887 
##    inode3219    inode3238    inode3239    inode3241    inode3242 
##    336290887    336290887    336290887    336290887    336290887 
##    inode3246    inode3259    inode3264    inode3269    inode3272 
##    336290887    336290887    336290887    336290887    336290887 
##    inode3274    inode3279    inode3280    inode3282    inode3284 
##    336290887    336290887    336290887    336290887    336290887 
##    inode3288    inode3290    inode3297    inode3301    inode3315 
##    336290887    336290887    336290887    336290887    336290887 
##    inode3316    inode3319    inode3326    inode3351    inode3490 
##    336290887    336290887    336290887    336290887    336290887 
##    inode3495    inode3496    inode3501    inode3502    inode3509 
##    336290887    336290887    336290887    336290887    336290887 
##    inode3513    inode3514    inode3525    inode3538    inode3542 
##    336290887    336290887    336290887    336290887    336290887 
##    inode3572    inode3631    inode3714    inode3732    inode3769 
##    336290887    336290887    336290887    336290887    336290887 
##    inode3970    inode4032    inode4086 
##    336290887    336290887    336290887 
## 
## The objective function may be at a saddle point -- check eigenvectors or try a simpler model
OU1_SVMP$eigval
## [1]  2.6e+01 -1.3e-07
OU1_SVMP$solution.se
##          -0.028600184 -0.160843603 -0.235324367 -0.314729465 -0.331612132
## alpha             NaN          NaN          NaN          NaN          NaN
## sigma.sq    0.1961173    0.1961173    0.1961173    0.1961173    0.1961173
##          -0.334277933 -0.336945636 -0.337468929 -0.399213836 -0.399284019
## alpha             NaN          NaN          NaN          NaN          NaN
## sigma.sq    0.1961173    0.1961173    0.1961173    0.1961173    0.1961173
##          -0.4034999 -0.454790159 -0.483120435 -0.498780177 -0.508750647
## alpha           NaN          NaN          NaN          NaN          NaN
## sigma.sq  0.1961173    0.1961173    0.1961173    0.1961173    0.1961173
##          -0.556403047 -0.563339519 -0.612242656 0.24612442 0.688226777
## alpha             NaN          NaN          NaN        NaN         NaN
## sigma.sq    0.1961173    0.1961173    0.1961173  0.1961173   0.1961173
##          0.716248171 0.800457806 0.852053529 0.884429117 1.105054626
## alpha            NaN         NaN         NaN         NaN         NaN
## sigma.sq   0.1961173   0.1961173   0.1961173   0.1961173   0.1961173
##          1.501471811 1.730054146 1.739986761 1.938191918 2.055614142
## alpha            NaN         NaN         NaN         NaN         NaN
## sigma.sq   0.1961173   0.1961173   0.1961173   0.1961173   0.1961173
##          2.13114086 2.347170187 2.350545516 2.38904884 2.485664868
## alpha           NaN         NaN         NaN        NaN         NaN
## sigma.sq  0.1961173   0.1961173   0.1961173  0.1961173   0.1961173
##          2.505774697 2.566762637 2.574411326 2.706669156 2.712007513
## alpha            NaN         NaN         NaN         NaN         NaN
## sigma.sq   0.1961173   0.1961173   0.1961173   0.1961173   0.1961173
##          2.722965014 2.732313956 2.73286191 2.751484952 2.753080674
## alpha            NaN         NaN        NaN         NaN         NaN
## sigma.sq   0.1961173   0.1961173  0.1961173   0.1961173   0.1961173
##          2.760067398 2.774368128 2.795360528 2.803163813 2.806058383
## alpha            NaN         NaN         NaN         NaN         NaN
## sigma.sq   0.1961173   0.1961173   0.1961173   0.1961173   0.1961173
##          2.821722852 2.840055323 inode3122 inode3123 inode3151 inode3159
## alpha            NaN         NaN       NaN       NaN       NaN       NaN
## sigma.sq   0.1961173   0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## alpha          NaN       NaN       NaN       NaN       NaN       NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## alpha          NaN       NaN       NaN       NaN       NaN       NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## alpha          NaN       NaN       NaN       NaN       NaN       NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## alpha          NaN       NaN       NaN       NaN       NaN       NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## alpha          NaN       NaN       NaN       NaN       NaN       NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## alpha          NaN       NaN       NaN       NaN       NaN       NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## alpha          NaN       NaN       NaN       NaN       NaN       NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
##          inode3732 inode3769 inode3970 inode4032 inode4086
## alpha          NaN       NaN       NaN       NaN       NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173

OUM

OUM_SVMP<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OUM_SVMP
## 
## Fit
##       lnL     AIC     AICc      BIC model ntax
##  -79.2955 176.591 180.8767 194.1522   OUM   52
## 
## 
## Rates
##                  1         2         3         4         5         6
## alpha    0.2779875 0.2779875 0.2779875 0.2779875 0.2779875 0.2779875
## sigma.sq 0.6909299 0.6909299 0.6909299 0.6909299 0.6909299 0.6909299
##                  7
## alpha    0.2779875
## sigma.sq 0.6909299
## 
## Optima
##                 1        2         3         4         5         6
## estimate 9.031596 2.315193 4.0468147 0.7470476 2.3892583 1.0004442
## se       1.954092 2.256422 0.2455787 2.2651647 0.3627398 0.8008283
##                   7
## estimate -0.9307609
## se        0.3368008
## 
## 
## Half life (another way of reporting alpha)
##        1        2        3        4        5        6        7 
## 2.493447 2.493447 2.493447 2.493447 2.493447 2.493447 2.493447 
## 
## Arrived at a reliable solution

AIC

aic<-setNames(c(BM1_SVMP$AICc,OU1_SVMP$AICc,OUM_SVMP$AICc),
              c("BM","OU1","OUM"))
aic
##       BM      OU1      OUM 
## 191.1388 193.3939 180.8767
aic.w(aic)
##         BM        OU1        OUM 
## 0.00586446 0.00189906 0.99223648

vPLA2

dat<-read.csv("./data/Ouwie_data/vPLA2_OUwie_ManyOptions_optima.csv")

BM

BM1_vPLA2<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
BM1_vPLA2
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 158.2624 158.5073 162.1649   BM1   52
## 
## Rates
##          -0.05037806 -0.05558464 -0.128998329 -0.19150365 -0.214161925
## alpha             NA          NA           NA          NA           NA
## sigma.sq  0.04805937  0.04805937   0.04805937  0.04805937   0.04805937
##          -0.260215768 -0.273551879 -0.327981232 -0.334277933 -0.347029762
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.359161832 -0.364412135 -0.375611762 -0.380235729 -0.399213836
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.399284019 -0.408989879 -0.445499084 -0.454790159 -0.456943595
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.463327573 -0.463654083 -0.473209269 -0.483120435 -0.505966472
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.539435104 -0.563339519 -0.612216239 -0.612242656 -0.61894364
## alpha              NA           NA           NA           NA          NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937  0.04805937
##          -0.705954615 0.030183724 0.086301032 0.173260936 0.197482907
## alpha              NA          NA          NA          NA          NA
## sigma.sq   0.04805937  0.04805937  0.04805937  0.04805937  0.04805937
##          0.289149918 0.305865064 0.641462714 0.718516561 0.968893752
## alpha             NA          NA          NA          NA          NA
## sigma.sq  0.04805937  0.04805937  0.04805937  0.04805937  0.04805937
##          1.232175577 1.234150763 1.318284305 1.335952395 1.620250928
## alpha             NA          NA          NA          NA          NA
## sigma.sq  0.04805937  0.04805937  0.04805937  0.04805937  0.04805937
##          1.928659323 2.007079893 2.463355156 2.532379278 2.559969588
## alpha             NA          NA          NA          NA          NA
## sigma.sq  0.04805937  0.04805937  0.04805937  0.04805937  0.04805937
##          2.831003753 2.841994278  inode3122  inode3123  inode3151
## alpha             NA          NA         NA         NA         NA
## sigma.sq  0.04805937  0.04805937 0.04805937 0.04805937 0.04805937
##           inode3159  inode3160  inode3162  inode3217  inode3218  inode3219
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3238  inode3239  inode3241  inode3242  inode3246  inode3259
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3264  inode3269  inode3272  inode3274  inode3279  inode3280
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3282  inode3284  inode3288  inode3290  inode3297  inode3301
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3315  inode3316  inode3319  inode3326  inode3351  inode3490
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3495  inode3496  inode3501  inode3502  inode3509  inode3513
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3514  inode3525  inode3538  inode3542  inode3572  inode3631
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3714  inode3732  inode3769  inode3970  inode4032  inode4086
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 
## Optima
##          -0.05037806 -0.05558464 -0.128998329 -0.19150365 -0.214161925
## estimate   4.0576335           0            0           0            0
## se         0.7261147           0            0           0            0
##          -0.260215768 -0.273551879 -0.327981232 -0.334277933 -0.347029762
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.359161832 -0.364412135 -0.375611762 -0.380235729 -0.399213836
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.399284019 -0.408989879 -0.445499084 -0.454790159 -0.456943595
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.463327573 -0.463654083 -0.473209269 -0.483120435 -0.505966472
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.539435104 -0.563339519 -0.612216239 -0.612242656 -0.61894364
## estimate            0            0            0            0           0
## se                  0            0            0            0           0
##          -0.705954615 0.030183724 0.086301032 0.173260936 0.197482907
## estimate            0           0           0           0           0
## se                  0           0           0           0           0
##          0.289149918 0.305865064 0.641462714 0.718516561 0.968893752
## estimate           0           0           0           0           0
## se                 0           0           0           0           0
##          1.232175577 1.234150763 1.318284305 1.335952395 1.620250928
## estimate           0           0           0           0           0
## se                 0           0           0           0           0
##          1.928659323 2.007079893 2.463355156 2.532379278 2.559969588
## estimate           0           0           0           0           0
## se                 0           0           0           0           0
##          2.831003753 2.841994278 inode3122 inode3123 inode3151 inode3159
## estimate           0           0         0         0         0         0
## se                 0           0         0         0         0         0
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate         0         0         0         0         0
## se               0         0         0         0         0
## 
## Arrived at a reliable solution

OU1

OU1_vPLA2<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OU1_vPLA2
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 160.2624 160.7624 166.1161   OU1   52
## 
## Rates
##           -0.05037806  -0.05558464 -0.128998329  -0.19150365 -0.214161925
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.260215768 -0.273551879 -0.327981232 -0.334277933 -0.347029762
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.359161832 -0.364412135 -0.375611762 -0.380235729 -0.399213836
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.399284019 -0.408989879 -0.445499084 -0.454790159 -0.456943595
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.463327573 -0.463654083 -0.473209269 -0.483120435 -0.505966472
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.539435104 -0.563339519 -0.612216239 -0.612242656  -0.61894364
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.705954615  0.030183724  0.086301032  0.173260936  0.197482907
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           0.289149918  0.305865064  0.641462714  0.718516561  0.968893752
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           1.232175577  1.234150763  1.318284305  1.335952395  1.620250928
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           1.928659323  2.007079893  2.463355156  2.532379278  2.559969588
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           2.831003753  2.841994278    inode3122    inode3123    inode3151
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3159    inode3160    inode3162    inode3217    inode3218
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3219    inode3238    inode3239    inode3241    inode3242
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3246    inode3259    inode3264    inode3269    inode3272
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3274    inode3279    inode3280    inode3282    inode3284
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3288    inode3290    inode3297    inode3301    inode3315
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3316    inode3319    inode3326    inode3351    inode3490
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3495    inode3496    inode3501    inode3502    inode3509
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3513    inode3514    inode3525    inode3538    inode3542
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3572    inode3631    inode3714    inode3732    inode3769
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3970    inode4032    inode4086
## alpha    2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
## 
## 
## Optima
##          -0.05037806 -0.05558464 -0.128998329 -0.19150365 -0.214161925
## estimate   4.0576335   4.0576335    4.0576335   4.0576335    4.0576335
## se         0.7260536   0.7260536    0.7260536   0.7260536    0.7260536
##          -0.260215768 -0.273551879 -0.327981232 -0.334277933 -0.347029762
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.359161832 -0.364412135 -0.375611762 -0.380235729 -0.399213836
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.399284019 -0.408989879 -0.445499084 -0.454790159 -0.456943595
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.463327573 -0.463654083 -0.473209269 -0.483120435 -0.505966472
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.539435104 -0.563339519 -0.612216239 -0.612242656 -0.61894364
## estimate    4.0576335    4.0576335    4.0576335    4.0576335   4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536   0.7260536
##          -0.705954615 0.030183724 0.086301032 0.173260936 0.197482907
## estimate    4.0576335   4.0576335   4.0576335   4.0576335   4.0576335
## se          0.7260536   0.7260536   0.7260536   0.7260536   0.7260536
##          0.289149918 0.305865064 0.641462714 0.718516561 0.968893752
## estimate   4.0576335   4.0576335   4.0576335   4.0576335   4.0576335
## se         0.7260536   0.7260536   0.7260536   0.7260536   0.7260536
##          1.232175577 1.234150763 1.318284305 1.335952395 1.620250928
## estimate   4.0576335   4.0576335   4.0576335   4.0576335   4.0576335
## se         0.7260536   0.7260536   0.7260536   0.7260536   0.7260536
##          1.928659323 2.007079893 2.463355156 2.532379278 2.559969588
## estimate   4.0576335   4.0576335   4.0576335   4.0576335   4.0576335
## se         0.7260536   0.7260536   0.7260536   0.7260536   0.7260536
##          2.831003753 2.841994278 inode3122 inode3123 inode3151 inode3159
## estimate   4.0576335   4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se         0.7260536   0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 
## 
## Half life (another way of reporting alpha)
##  -0.05037806  -0.05558464 -0.128998329  -0.19150365 -0.214161925 
##    308643937    308643937    308643937    308643937    308643937 
## -0.260215768 -0.273551879 -0.327981232 -0.334277933 -0.347029762 
##    308643937    308643937    308643937    308643937    308643937 
## -0.359161832 -0.364412135 -0.375611762 -0.380235729 -0.399213836 
##    308643937    308643937    308643937    308643937    308643937 
## -0.399284019 -0.408989879 -0.445499084 -0.454790159 -0.456943595 
##    308643937    308643937    308643937    308643937    308643937 
## -0.463327573 -0.463654083 -0.473209269 -0.483120435 -0.505966472 
##    308643937    308643937    308643937    308643937    308643937 
## -0.539435104 -0.563339519 -0.612216239 -0.612242656  -0.61894364 
##    308643937    308643937    308643937    308643937    308643937 
## -0.705954615  0.030183724  0.086301032  0.173260936  0.197482907 
##    308643937    308643937    308643937    308643937    308643937 
##  0.289149918  0.305865064  0.641462714  0.718516561  0.968893752 
##    308643937    308643937    308643937    308643937    308643937 
##  1.232175577  1.234150763  1.318284305  1.335952395  1.620250928 
##    308643937    308643937    308643937    308643937    308643937 
##  1.928659323  2.007079893  2.463355156  2.532379278  2.559969588 
##    308643937    308643937    308643937    308643937    308643937 
##  2.831003753  2.841994278    inode3122    inode3123    inode3151 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3159    inode3160    inode3162    inode3217    inode3218 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3219    inode3238    inode3239    inode3241    inode3242 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3246    inode3259    inode3264    inode3269    inode3272 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3274    inode3279    inode3280    inode3282    inode3284 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3288    inode3290    inode3297    inode3301    inode3315 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3316    inode3319    inode3326    inode3351    inode3490 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3495    inode3496    inode3501    inode3502    inode3509 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3513    inode3514    inode3525    inode3538    inode3542 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3572    inode3631    inode3714    inode3732    inode3769 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3970    inode4032    inode4086 
##    308643937    308643937    308643937 
## 
## Arrived at a reliable solution
OU1_vPLA2$eigval
## [1] 2.6e+01 1.3e-06
OU1_vPLA2$solution.se
##          -0.05037806 -0.05558464 -0.128998329 -0.19150365 -0.214161925
## alpha    882.7127566 882.7127566  882.7127566 882.7127566  882.7127566
## sigma.sq   0.1961103   0.1961103    0.1961103   0.1961103    0.1961103
##          -0.260215768 -0.273551879 -0.327981232 -0.334277933 -0.347029762
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.359161832 -0.364412135 -0.375611762 -0.380235729 -0.399213836
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.399284019 -0.408989879 -0.445499084 -0.454790159 -0.456943595
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.463327573 -0.463654083 -0.473209269 -0.483120435 -0.505966472
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.539435104 -0.563339519 -0.612216239 -0.612242656 -0.61894364
## alpha     882.7127566  882.7127566  882.7127566  882.7127566 882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103   0.1961103
##          -0.705954615 0.030183724 0.086301032 0.173260936 0.197482907
## alpha     882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq    0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##          0.289149918 0.305865064 0.641462714 0.718516561 0.968893752
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##          1.232175577 1.234150763 1.318284305 1.335952395 1.620250928
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##          1.928659323 2.007079893 2.463355156 2.532379278 2.559969588
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##          2.831003753 2.841994278   inode3122   inode3123   inode3151
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3159   inode3160   inode3162   inode3217   inode3218
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3219   inode3238   inode3239   inode3241   inode3242
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3246   inode3259   inode3264   inode3269   inode3272
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3274   inode3279   inode3280   inode3282   inode3284
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3288   inode3290   inode3297   inode3301   inode3315
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3316   inode3319   inode3326   inode3351   inode3490
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3495   inode3496   inode3501   inode3502   inode3509
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3513   inode3514   inode3525   inode3538   inode3542
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3572   inode3631   inode3714   inode3732   inode3769
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3970   inode4032   inode4086
## alpha    882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103

OUM

OUM_vPLA2<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OUM_vPLA2
## 
## Fit
##       lnL       AIC     AICc       BIC model ntax
##  85.24088 -152.4818 -148.196 -134.9206   OUM   52
## 
## 
## Rates
##                   1          2          3          4          5          6
## alpha    5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
##                   7
## alpha    5.78373949
## sigma.sq 0.02552326
## 
## Optima
##                   1          2          3          4          5          6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se       0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
##                   7
## estimate 6.99998674
## se       0.01485411
## 
## 
## Half life (another way of reporting alpha)
##         1         2         3         4         5         6         7 
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 
## 
## Arrived at a reliable solution

AIC

aic<-setNames(c(BM1_vPLA2$AICc,OU1_vPLA2$AICc,OUM_vPLA2$AICc),
              c("BM","OU1","OUM"))
aic
##        BM       OU1       OUM 
##  158.5073  160.7624 -148.1960
aic.w(aic)
##  BM OU1 OUM 
##   0   0   1

ePLA2

dat<-read.csv("./data/Ouwie_data/ePLA2_OUwie_ManyOptions_optima.csv")

BM

BM1_ePLA2<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
BM1_ePLA2
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 158.2624 158.5073 162.1649   BM1   52
## 
## Rates
##          -0.080031991 -0.177729566 -0.288225932 -0.325407223 -0.336320973
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.343935613 -0.347029762 -0.36429282 -0.422992017 -0.425565648
## alpha              NA           NA          NA           NA           NA
## sigma.sq   0.04805937   0.04805937  0.04805937   0.04805937   0.04805937
##          -0.428224485 -0.449261397 -0.461474263 -0.463654083 -0.466734078
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.467614451 -0.478411682 -0.494906486 -0.496800054 -0.52278517
## alpha              NA           NA           NA           NA          NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937  0.04805937
##          -0.523308863 -0.527913521 -0.535408592 -0.539435104 -0.542252225
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.555961591 -0.569277353 -0.581015956 -0.581916282 -0.603132172
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.612216239 -0.632877207 -0.657107195 -0.665162495 -0.684832772
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.709372748 -0.731309262 -0.794196933 -0.827893652 -0.900691872
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.96572225 0.148517432 0.363798869 0.379063726 0.451182501
## alpha             NA          NA          NA          NA          NA
## sigma.sq  0.04805937  0.04805937  0.04805937  0.04805937  0.04805937
##          0.840437155 1.216401792 1.559973376 1.977427802 2.414894519
## alpha             NA          NA          NA          NA          NA
## sigma.sq  0.04805937  0.04805937  0.04805937  0.04805937  0.04805937
##          2.647357137 2.799948184  inode3122  inode3123  inode3151
## alpha             NA          NA         NA         NA         NA
## sigma.sq  0.04805937  0.04805937 0.04805937 0.04805937 0.04805937
##           inode3159  inode3160  inode3162  inode3217  inode3218  inode3219
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3238  inode3239  inode3241  inode3242  inode3246  inode3259
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3264  inode3269  inode3272  inode3274  inode3279  inode3280
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3282  inode3284  inode3288  inode3290  inode3297  inode3301
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3315  inode3316  inode3319  inode3326  inode3351  inode3490
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3495  inode3496  inode3501  inode3502  inode3509  inode3513
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3514  inode3525  inode3538  inode3542  inode3572  inode3631
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3714  inode3732  inode3769  inode3970  inode4032  inode4086
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 
## Optima
##          -0.080031991 -0.177729566 -0.288225932 -0.325407223 -0.336320973
## estimate    4.0576335            0            0            0            0
## se          0.7261147            0            0            0            0
##          -0.343935613 -0.347029762 -0.36429282 -0.422992017 -0.425565648
## estimate            0            0           0            0            0
## se                  0            0           0            0            0
##          -0.428224485 -0.449261397 -0.461474263 -0.463654083 -0.466734078
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.467614451 -0.478411682 -0.494906486 -0.496800054 -0.52278517
## estimate            0            0            0            0           0
## se                  0            0            0            0           0
##          -0.523308863 -0.527913521 -0.535408592 -0.539435104 -0.542252225
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.555961591 -0.569277353 -0.581015956 -0.581916282 -0.603132172
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.612216239 -0.632877207 -0.657107195 -0.665162495 -0.684832772
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.709372748 -0.731309262 -0.794196933 -0.827893652 -0.900691872
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.96572225 0.148517432 0.363798869 0.379063726 0.451182501
## estimate           0           0           0           0           0
## se                 0           0           0           0           0
##          0.840437155 1.216401792 1.559973376 1.977427802 2.414894519
## estimate           0           0           0           0           0
## se                 0           0           0           0           0
##          2.647357137 2.799948184 inode3122 inode3123 inode3151 inode3159
## estimate           0           0         0         0         0         0
## se                 0           0         0         0         0         0
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate         0         0         0         0         0
## se               0         0         0         0         0
## 
## Arrived at a reliable solution

OU1

OU1_ePLA2<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OU1_ePLA2
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 160.2624 160.7624 166.1161   OU1   52
## 
## Rates
##          -0.080031991 -0.177729566 -0.288225932 -0.325407223 -0.336320973
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.343935613 -0.347029762  -0.36429282 -0.422992017 -0.425565648
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.428224485 -0.449261397 -0.461474263 -0.463654083 -0.466734078
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.467614451 -0.478411682 -0.494906486 -0.496800054  -0.52278517
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.523308863 -0.527913521 -0.535408592 -0.539435104 -0.542252225
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.555961591 -0.569277353 -0.581015956 -0.581916282 -0.603132172
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.612216239 -0.632877207 -0.657107195 -0.665162495 -0.684832772
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.709372748 -0.731309262 -0.794196933 -0.827893652 -0.900691872
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           -0.96572225  0.148517432  0.363798869  0.379063726  0.451182501
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           0.840437155  1.216401792  1.559973376  1.977427802  2.414894519
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           2.647357137  2.799948184    inode3122    inode3123    inode3151
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3159    inode3160    inode3162    inode3217    inode3218
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3219    inode3238    inode3239    inode3241    inode3242
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3246    inode3259    inode3264    inode3269    inode3272
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3274    inode3279    inode3280    inode3282    inode3284
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3288    inode3290    inode3297    inode3301    inode3315
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3316    inode3319    inode3326    inode3351    inode3490
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3495    inode3496    inode3501    inode3502    inode3509
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3513    inode3514    inode3525    inode3538    inode3542
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3572    inode3631    inode3714    inode3732    inode3769
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3970    inode4032    inode4086
## alpha    2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
## 
## 
## Optima
##          -0.080031991 -0.177729566 -0.288225932 -0.325407223 -0.336320973
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.343935613 -0.347029762 -0.36429282 -0.422992017 -0.425565648
## estimate    4.0576335    4.0576335   4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536   0.7260536    0.7260536    0.7260536
##          -0.428224485 -0.449261397 -0.461474263 -0.463654083 -0.466734078
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.467614451 -0.478411682 -0.494906486 -0.496800054 -0.52278517
## estimate    4.0576335    4.0576335    4.0576335    4.0576335   4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536   0.7260536
##          -0.523308863 -0.527913521 -0.535408592 -0.539435104 -0.542252225
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.555961591 -0.569277353 -0.581015956 -0.581916282 -0.603132172
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.612216239 -0.632877207 -0.657107195 -0.665162495 -0.684832772
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.709372748 -0.731309262 -0.794196933 -0.827893652 -0.900691872
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.96572225 0.148517432 0.363798869 0.379063726 0.451182501
## estimate   4.0576335   4.0576335   4.0576335   4.0576335   4.0576335
## se         0.7260536   0.7260536   0.7260536   0.7260536   0.7260536
##          0.840437155 1.216401792 1.559973376 1.977427802 2.414894519
## estimate   4.0576335   4.0576335   4.0576335   4.0576335   4.0576335
## se         0.7260536   0.7260536   0.7260536   0.7260536   0.7260536
##          2.647357137 2.799948184 inode3122 inode3123 inode3151 inode3159
## estimate   4.0576335   4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se         0.7260536   0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 
## 
## Half life (another way of reporting alpha)
## -0.080031991 -0.177729566 -0.288225932 -0.325407223 -0.336320973 
##    308643937    308643937    308643937    308643937    308643937 
## -0.343935613 -0.347029762  -0.36429282 -0.422992017 -0.425565648 
##    308643937    308643937    308643937    308643937    308643937 
## -0.428224485 -0.449261397 -0.461474263 -0.463654083 -0.466734078 
##    308643937    308643937    308643937    308643937    308643937 
## -0.467614451 -0.478411682 -0.494906486 -0.496800054  -0.52278517 
##    308643937    308643937    308643937    308643937    308643937 
## -0.523308863 -0.527913521 -0.535408592 -0.539435104 -0.542252225 
##    308643937    308643937    308643937    308643937    308643937 
## -0.555961591 -0.569277353 -0.581015956 -0.581916282 -0.603132172 
##    308643937    308643937    308643937    308643937    308643937 
## -0.612216239 -0.632877207 -0.657107195 -0.665162495 -0.684832772 
##    308643937    308643937    308643937    308643937    308643937 
## -0.709372748 -0.731309262 -0.794196933 -0.827893652 -0.900691872 
##    308643937    308643937    308643937    308643937    308643937 
##  -0.96572225  0.148517432  0.363798869  0.379063726  0.451182501 
##    308643937    308643937    308643937    308643937    308643937 
##  0.840437155  1.216401792  1.559973376  1.977427802  2.414894519 
##    308643937    308643937    308643937    308643937    308643937 
##  2.647357137  2.799948184    inode3122    inode3123    inode3151 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3159    inode3160    inode3162    inode3217    inode3218 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3219    inode3238    inode3239    inode3241    inode3242 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3246    inode3259    inode3264    inode3269    inode3272 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3274    inode3279    inode3280    inode3282    inode3284 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3288    inode3290    inode3297    inode3301    inode3315 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3316    inode3319    inode3326    inode3351    inode3490 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3495    inode3496    inode3501    inode3502    inode3509 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3513    inode3514    inode3525    inode3538    inode3542 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3572    inode3631    inode3714    inode3732    inode3769 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3970    inode4032    inode4086 
##    308643937    308643937    308643937 
## 
## Arrived at a reliable solution
OU1_ePLA2$eigval
## [1] 2.6e+01 1.3e-06
OU1_ePLA2$solution.se
##          -0.080031991 -0.177729566 -0.288225932 -0.325407223 -0.336320973
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.343935613 -0.347029762 -0.36429282 -0.422992017 -0.425565648
## alpha     882.7127566  882.7127566 882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103   0.1961103    0.1961103    0.1961103
##          -0.428224485 -0.449261397 -0.461474263 -0.463654083 -0.466734078
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.467614451 -0.478411682 -0.494906486 -0.496800054 -0.52278517
## alpha     882.7127566  882.7127566  882.7127566  882.7127566 882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103   0.1961103
##          -0.523308863 -0.527913521 -0.535408592 -0.539435104 -0.542252225
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.555961591 -0.569277353 -0.581015956 -0.581916282 -0.603132172
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.612216239 -0.632877207 -0.657107195 -0.665162495 -0.684832772
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.709372748 -0.731309262 -0.794196933 -0.827893652 -0.900691872
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.96572225 0.148517432 0.363798869 0.379063726 0.451182501
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##          0.840437155 1.216401792 1.559973376 1.977427802 2.414894519
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##          2.647357137 2.799948184   inode3122   inode3123   inode3151
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3159   inode3160   inode3162   inode3217   inode3218
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3219   inode3238   inode3239   inode3241   inode3242
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3246   inode3259   inode3264   inode3269   inode3272
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3274   inode3279   inode3280   inode3282   inode3284
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3288   inode3290   inode3297   inode3301   inode3315
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3316   inode3319   inode3326   inode3351   inode3490
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3495   inode3496   inode3501   inode3502   inode3509
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3513   inode3514   inode3525   inode3538   inode3542
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3572   inode3631   inode3714   inode3732   inode3769
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3970   inode4032   inode4086
## alpha    882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103

OUM

OUM_ePLA2<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OUM_ePLA2
## 
## Fit
##       lnL       AIC     AICc       BIC model ntax
##  85.24088 -152.4818 -148.196 -134.9206   OUM   52
## 
## 
## Rates
##                   1          2          3          4          5          6
## alpha    5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
##                   7
## alpha    5.78373949
## sigma.sq 0.02552326
## 
## Optima
##                   1          2          3          4          5          6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se       0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
##                   7
## estimate 6.99998674
## se       0.01485411
## 
## 
## Half life (another way of reporting alpha)
##         1         2         3         4         5         6         7 
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 
## 
## Arrived at a reliable solution

AIC

aic<-setNames(c(BM1_ePLA2$AICc,OU1_ePLA2$AICc,OUM_ePLA2$AICc),
              c("BM","OU1","OUM"))
aic
##        BM       OU1       OUM 
##  158.5073  160.7624 -148.1960
aic.w(aic)
##  BM OU1 OUM 
##   0   0   1

CRISP

dat<-read.csv("./data/Ouwie_data/CRISP_OUwie_ManyOptions_optima.csv")

BM

BM1_CRISP<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
BM1_CRISP
## 
## Fit
##       lnL     AIC     AICc      BIC model ntax
##  -137.289 278.578 278.8229 282.4805   BM1   52
## 
## Rates
##          -0.00423934 -0.175256643 -0.188704348 -0.19150365 -0.230786313
## alpha             NA           NA           NA          NA           NA
## sigma.sq   0.4859955    0.4859955    0.4859955   0.4859955    0.4859955
##          -0.275282586 -0.285641449 -0.30479064 -0.325766959 -0.343935613
## alpha              NA           NA          NA           NA           NA
## sigma.sq    0.4859955    0.4859955   0.4859955    0.4859955    0.4859955
##          -0.347144146 -0.348993029 -0.359161832 -0.361858128 -0.363737891
## alpha              NA           NA           NA           NA           NA
## sigma.sq    0.4859955    0.4859955    0.4859955    0.4859955    0.4859955
##          -0.364251376 -0.371802781 -0.380235729 -0.3861934 -0.399213836
## alpha              NA           NA           NA         NA           NA
## sigma.sq    0.4859955    0.4859955    0.4859955  0.4859955    0.4859955
##          -0.401335606 -0.412305063 -0.415183185 -0.421663658 -0.422514101
## alpha              NA           NA           NA           NA           NA
## sigma.sq    0.4859955    0.4859955    0.4859955    0.4859955    0.4859955
##          -0.422992017 -0.423308801 -0.445491375 -0.448434866 -0.452125326
## alpha              NA           NA           NA           NA           NA
## sigma.sq    0.4859955    0.4859955    0.4859955    0.4859955    0.4859955
##          -0.454790159 -0.466734078 -0.473209269 -0.505966472 -0.512396631
## alpha              NA           NA           NA           NA           NA
## sigma.sq    0.4859955    0.4859955    0.4859955    0.4859955    0.4859955
##          -0.517082249 -0.543732229 -0.552677293 -0.555961591 -0.581015956
## alpha              NA           NA           NA           NA           NA
## sigma.sq    0.4859955    0.4859955    0.4859955    0.4859955    0.4859955
##          -0.585182207 -0.590292055 -0.632877207 -0.655609114 -0.705954615
## alpha              NA           NA           NA           NA           NA
## sigma.sq    0.4859955    0.4859955    0.4859955    0.4859955    0.4859955
##          -0.773362074 -0.900691872 0.046644937 0.077062158 0.079914355
## alpha              NA           NA          NA          NA          NA
## sigma.sq    0.4859955    0.4859955   0.4859955   0.4859955   0.4859955
##          0.146321473 0.317538642 inode3122 inode3123 inode3151 inode3159
## alpha             NA          NA        NA        NA        NA        NA
## sigma.sq   0.4859955   0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## alpha           NA        NA        NA        NA        NA        NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## alpha           NA        NA        NA        NA        NA        NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## alpha           NA        NA        NA        NA        NA        NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## alpha           NA        NA        NA        NA        NA        NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## alpha           NA        NA        NA        NA        NA        NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## alpha           NA        NA        NA        NA        NA        NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## alpha           NA        NA        NA        NA        NA        NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
##          inode3732 inode3769 inode3970 inode4032 inode4086
## alpha           NA        NA        NA        NA        NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## 
## Optima
##          -0.00423934 -0.175256643 -0.188704348 -0.19150365 -0.230786313
## estimate  -0.8351102            0            0           0            0
## se         2.3090445            0            0           0            0
##          -0.275282586 -0.285641449 -0.30479064 -0.325766959 -0.343935613
## estimate            0            0           0            0            0
## se                  0            0           0            0            0
##          -0.347144146 -0.348993029 -0.359161832 -0.361858128 -0.363737891
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.364251376 -0.371802781 -0.380235729 -0.3861934 -0.399213836
## estimate            0            0            0          0            0
## se                  0            0            0          0            0
##          -0.401335606 -0.412305063 -0.415183185 -0.421663658 -0.422514101
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.422992017 -0.423308801 -0.445491375 -0.448434866 -0.452125326
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.454790159 -0.466734078 -0.473209269 -0.505966472 -0.512396631
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.517082249 -0.543732229 -0.552677293 -0.555961591 -0.581015956
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.585182207 -0.590292055 -0.632877207 -0.655609114 -0.705954615
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.773362074 -0.900691872 0.046644937 0.077062158 0.079914355
## estimate            0            0           0           0           0
## se                  0            0           0           0           0
##          0.146321473 0.317538642 inode3122 inode3123 inode3151 inode3159
## estimate           0           0         0         0         0         0
## se                 0           0         0         0         0         0
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate         0         0         0         0         0
## se               0         0         0         0         0
## 
## Arrived at a reliable solution

OU1

OU1_CRISP<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OU1_CRISP
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -133.7486 273.4972 273.9972 279.3509   OU1   52
## 
## Rates
##          -0.00423934 -0.175256643 -0.188704348 -0.19150365 -0.230786313
## alpha     0.04184785   0.04184785   0.04184785  0.04184785   0.04184785
## sigma.sq  1.03527654   1.03527654   1.03527654  1.03527654   1.03527654
##          -0.275282586 -0.285641449 -0.30479064 -0.325766959 -0.343935613
## alpha      0.04184785   0.04184785  0.04184785   0.04184785   0.04184785
## sigma.sq   1.03527654   1.03527654  1.03527654   1.03527654   1.03527654
##          -0.347144146 -0.348993029 -0.359161832 -0.361858128 -0.363737891
## alpha      0.04184785   0.04184785   0.04184785   0.04184785   0.04184785
## sigma.sq   1.03527654   1.03527654   1.03527654   1.03527654   1.03527654
##          -0.364251376 -0.371802781 -0.380235729 -0.3861934 -0.399213836
## alpha      0.04184785   0.04184785   0.04184785 0.04184785   0.04184785
## sigma.sq   1.03527654   1.03527654   1.03527654 1.03527654   1.03527654
##          -0.401335606 -0.412305063 -0.415183185 -0.421663658 -0.422514101
## alpha      0.04184785   0.04184785   0.04184785   0.04184785   0.04184785
## sigma.sq   1.03527654   1.03527654   1.03527654   1.03527654   1.03527654
##          -0.422992017 -0.423308801 -0.445491375 -0.448434866 -0.452125326
## alpha      0.04184785   0.04184785   0.04184785   0.04184785   0.04184785
## sigma.sq   1.03527654   1.03527654   1.03527654   1.03527654   1.03527654
##          -0.454790159 -0.466734078 -0.473209269 -0.505966472 -0.512396631
## alpha      0.04184785   0.04184785   0.04184785   0.04184785   0.04184785
## sigma.sq   1.03527654   1.03527654   1.03527654   1.03527654   1.03527654
##          -0.517082249 -0.543732229 -0.552677293 -0.555961591 -0.581015956
## alpha      0.04184785   0.04184785   0.04184785   0.04184785   0.04184785
## sigma.sq   1.03527654   1.03527654   1.03527654   1.03527654   1.03527654
##          -0.585182207 -0.590292055 -0.632877207 -0.655609114 -0.705954615
## alpha      0.04184785   0.04184785   0.04184785   0.04184785   0.04184785
## sigma.sq   1.03527654   1.03527654   1.03527654   1.03527654   1.03527654
##          -0.773362074 -0.900691872 0.046644937 0.077062158 0.079914355
## alpha      0.04184785   0.04184785  0.04184785  0.04184785  0.04184785
## sigma.sq   1.03527654   1.03527654  1.03527654  1.03527654  1.03527654
##          0.146321473 0.317538642  inode3122  inode3123  inode3151
## alpha     0.04184785  0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq  1.03527654  1.03527654 1.03527654 1.03527654 1.03527654
##           inode3159  inode3160  inode3162  inode3217  inode3218  inode3219
## alpha    0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
##           inode3238  inode3239  inode3241  inode3242  inode3246  inode3259
## alpha    0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
##           inode3264  inode3269  inode3272  inode3274  inode3279  inode3280
## alpha    0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
##           inode3282  inode3284  inode3288  inode3290  inode3297  inode3301
## alpha    0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
##           inode3315  inode3316  inode3319  inode3326  inode3351  inode3490
## alpha    0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
##           inode3495  inode3496  inode3501  inode3502  inode3509  inode3513
## alpha    0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
##           inode3514  inode3525  inode3538  inode3542  inode3572  inode3631
## alpha    0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
##           inode3714  inode3732  inode3769  inode3970  inode4032  inode4086
## alpha    0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## 
## 
## Optima
##          -0.00423934 -0.175256643 -0.188704348 -0.19150365 -0.230786313
## estimate  -0.9053855   -0.9053855   -0.9053855  -0.9053855   -0.9053855
## se         0.7758632    0.7758632    0.7758632   0.7758632    0.7758632
##          -0.275282586 -0.285641449 -0.30479064 -0.325766959 -0.343935613
## estimate   -0.9053855   -0.9053855  -0.9053855   -0.9053855   -0.9053855
## se          0.7758632    0.7758632   0.7758632    0.7758632    0.7758632
##          -0.347144146 -0.348993029 -0.359161832 -0.361858128 -0.363737891
## estimate   -0.9053855   -0.9053855   -0.9053855   -0.9053855   -0.9053855
## se          0.7758632    0.7758632    0.7758632    0.7758632    0.7758632
##          -0.364251376 -0.371802781 -0.380235729 -0.3861934 -0.399213836
## estimate   -0.9053855   -0.9053855   -0.9053855 -0.9053855   -0.9053855
## se          0.7758632    0.7758632    0.7758632  0.7758632    0.7758632
##          -0.401335606 -0.412305063 -0.415183185 -0.421663658 -0.422514101
## estimate   -0.9053855   -0.9053855   -0.9053855   -0.9053855   -0.9053855
## se          0.7758632    0.7758632    0.7758632    0.7758632    0.7758632
##          -0.422992017 -0.423308801 -0.445491375 -0.448434866 -0.452125326
## estimate   -0.9053855   -0.9053855   -0.9053855   -0.9053855   -0.9053855
## se          0.7758632    0.7758632    0.7758632    0.7758632    0.7758632
##          -0.454790159 -0.466734078 -0.473209269 -0.505966472 -0.512396631
## estimate   -0.9053855   -0.9053855   -0.9053855   -0.9053855   -0.9053855
## se          0.7758632    0.7758632    0.7758632    0.7758632    0.7758632
##          -0.517082249 -0.543732229 -0.552677293 -0.555961591 -0.581015956
## estimate   -0.9053855   -0.9053855   -0.9053855   -0.9053855   -0.9053855
## se          0.7758632    0.7758632    0.7758632    0.7758632    0.7758632
##          -0.585182207 -0.590292055 -0.632877207 -0.655609114 -0.705954615
## estimate   -0.9053855   -0.9053855   -0.9053855   -0.9053855   -0.9053855
## se          0.7758632    0.7758632    0.7758632    0.7758632    0.7758632
##          -0.773362074 -0.900691872 0.046644937 0.077062158 0.079914355
## estimate   -0.9053855   -0.9053855  -0.9053855  -0.9053855  -0.9053855
## se          0.7758632    0.7758632   0.7758632   0.7758632   0.7758632
##          0.146321473 0.317538642  inode3122  inode3123  inode3151
## estimate  -0.9053855  -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se         0.7758632   0.7758632  0.7758632  0.7758632  0.7758632
##           inode3159  inode3160  inode3162  inode3217  inode3218  inode3219
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se        0.7758632  0.7758632  0.7758632  0.7758632  0.7758632  0.7758632
##           inode3238  inode3239  inode3241  inode3242  inode3246  inode3259
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se        0.7758632  0.7758632  0.7758632  0.7758632  0.7758632  0.7758632
##           inode3264  inode3269  inode3272  inode3274  inode3279  inode3280
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se        0.7758632  0.7758632  0.7758632  0.7758632  0.7758632  0.7758632
##           inode3282  inode3284  inode3288  inode3290  inode3297  inode3301
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se        0.7758632  0.7758632  0.7758632  0.7758632  0.7758632  0.7758632
##           inode3315  inode3316  inode3319  inode3326  inode3351  inode3490
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se        0.7758632  0.7758632  0.7758632  0.7758632  0.7758632  0.7758632
##           inode3495  inode3496  inode3501  inode3502  inode3509  inode3513
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se        0.7758632  0.7758632  0.7758632  0.7758632  0.7758632  0.7758632
##           inode3514  inode3525  inode3538  inode3542  inode3572  inode3631
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se        0.7758632  0.7758632  0.7758632  0.7758632  0.7758632  0.7758632
##           inode3714  inode3732  inode3769  inode3970  inode4032  inode4086
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se        0.7758632  0.7758632  0.7758632  0.7758632  0.7758632  0.7758632
## 
## 
## Half life (another way of reporting alpha)
##  -0.00423934 -0.175256643 -0.188704348  -0.19150365 -0.230786313 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
## -0.275282586 -0.285641449  -0.30479064 -0.325766959 -0.343935613 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
## -0.347144146 -0.348993029 -0.359161832 -0.361858128 -0.363737891 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
## -0.364251376 -0.371802781 -0.380235729   -0.3861934 -0.399213836 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
## -0.401335606 -0.412305063 -0.415183185 -0.421663658 -0.422514101 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
## -0.422992017 -0.423308801 -0.445491375 -0.448434866 -0.452125326 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
## -0.454790159 -0.466734078 -0.473209269 -0.505966472 -0.512396631 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
## -0.517082249 -0.543732229 -0.552677293 -0.555961591 -0.581015956 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
## -0.585182207 -0.590292055 -0.632877207 -0.655609114 -0.705954615 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
## -0.773362074 -0.900691872  0.046644937  0.077062158  0.079914355 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
##  0.146321473  0.317538642    inode3122    inode3123    inode3151 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
##    inode3159    inode3160    inode3162    inode3217    inode3218 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
##    inode3219    inode3238    inode3239    inode3241    inode3242 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
##    inode3246    inode3259    inode3264    inode3269    inode3272 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
##    inode3274    inode3279    inode3280    inode3282    inode3284 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
##    inode3288    inode3290    inode3297    inode3301    inode3315 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
##    inode3316    inode3319    inode3326    inode3351    inode3490 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
##    inode3495    inode3496    inode3501    inode3502    inode3509 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
##    inode3513    inode3514    inode3525    inode3538    inode3542 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
##    inode3572    inode3631    inode3714    inode3732    inode3769 
##     16.56351     16.56351     16.56351     16.56351     16.56351 
##    inode3970    inode4032    inode4086 
##     16.56351     16.56351     16.56351 
## 
## Arrived at a reliable solution
OU1_CRISP$eigval
## [1] 40.0  2.2
OU1_CRISP$solution.se
##          -0.00423934 -0.175256643 -0.188704348 -0.19150365 -0.230786313
## alpha      0.5508137    0.5508137    0.5508137   0.5508137    0.5508137
## sigma.sq   0.4314450    0.4314450    0.4314450   0.4314450    0.4314450
##          -0.275282586 -0.285641449 -0.30479064 -0.325766959 -0.343935613
## alpha       0.5508137    0.5508137   0.5508137    0.5508137    0.5508137
## sigma.sq    0.4314450    0.4314450   0.4314450    0.4314450    0.4314450
##          -0.347144146 -0.348993029 -0.359161832 -0.361858128 -0.363737891
## alpha       0.5508137    0.5508137    0.5508137    0.5508137    0.5508137
## sigma.sq    0.4314450    0.4314450    0.4314450    0.4314450    0.4314450
##          -0.364251376 -0.371802781 -0.380235729 -0.3861934 -0.399213836
## alpha       0.5508137    0.5508137    0.5508137  0.5508137    0.5508137
## sigma.sq    0.4314450    0.4314450    0.4314450  0.4314450    0.4314450
##          -0.401335606 -0.412305063 -0.415183185 -0.421663658 -0.422514101
## alpha       0.5508137    0.5508137    0.5508137    0.5508137    0.5508137
## sigma.sq    0.4314450    0.4314450    0.4314450    0.4314450    0.4314450
##          -0.422992017 -0.423308801 -0.445491375 -0.448434866 -0.452125326
## alpha       0.5508137    0.5508137    0.5508137    0.5508137    0.5508137
## sigma.sq    0.4314450    0.4314450    0.4314450    0.4314450    0.4314450
##          -0.454790159 -0.466734078 -0.473209269 -0.505966472 -0.512396631
## alpha       0.5508137    0.5508137    0.5508137    0.5508137    0.5508137
## sigma.sq    0.4314450    0.4314450    0.4314450    0.4314450    0.4314450
##          -0.517082249 -0.543732229 -0.552677293 -0.555961591 -0.581015956
## alpha       0.5508137    0.5508137    0.5508137    0.5508137    0.5508137
## sigma.sq    0.4314450    0.4314450    0.4314450    0.4314450    0.4314450
##          -0.585182207 -0.590292055 -0.632877207 -0.655609114 -0.705954615
## alpha       0.5508137    0.5508137    0.5508137    0.5508137    0.5508137
## sigma.sq    0.4314450    0.4314450    0.4314450    0.4314450    0.4314450
##          -0.773362074 -0.900691872 0.046644937 0.077062158 0.079914355
## alpha       0.5508137    0.5508137   0.5508137   0.5508137   0.5508137
## sigma.sq    0.4314450    0.4314450   0.4314450   0.4314450   0.4314450
##          0.146321473 0.317538642 inode3122 inode3123 inode3151 inode3159
## alpha      0.5508137   0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq   0.4314450   0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## alpha    0.5508137 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## alpha    0.5508137 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## alpha    0.5508137 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## alpha    0.5508137 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## alpha    0.5508137 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## alpha    0.5508137 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## alpha    0.5508137 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
##          inode3732 inode3769 inode3970 inode4032 inode4086
## alpha    0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450

OUM

OUM_CRISP<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OUM_CRISP
## 
## Fit
##        lnL      AIC     AICc     BIC model ntax
##  -130.0814 278.1628 282.4485 295.724   OUM   52
## 
## 
## Rates
##                   1          2          3          4          5          6
## alpha    0.07936546 0.07936546 0.07936546 0.07936546 0.07936546 0.07936546
## sigma.sq 1.49397240 1.49397240 1.49397240 1.49397240 1.49397240 1.49397240
##                   7
## alpha    0.07936546
## sigma.sq 1.49397240
## 
## Optima
##                 1         2          3         4         5         6
## estimate 17.60332 -3.376277 -0.4272226 -18.87897 -1.082753 -12.66602
## se       14.70393 15.399011  0.8541136  15.23660  1.272570   4.25283
##                   7
## estimate -1.4030843
## se        0.9571823
## 
## 
## Half life (another way of reporting alpha)
##        1        2        3        4        5        6        7 
## 8.733613 8.733613 8.733613 8.733613 8.733613 8.733613 8.733613 
## 
## Arrived at a reliable solution

AIC

aic<-setNames(c(BM1_CRISP$AICc,OU1_CRISP$AICc,OUM_CRISP$AICc),
              c("BM","OU1","OUM"))
aic
##       BM      OU1      OUM 
## 278.8229 273.9972 282.4485
aic.w(aic)
##         BM        OU1        OUM 
## 0.08110998 0.90565318 0.01323684

CTL

dat<-read.csv("./data/Ouwie_data/CTL_OUwie_ManyOptions_optima.csv")

BM

BM1_CTL<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
BM1_CTL
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 158.2624 158.5073 162.1649   BM1   52
## 
## Rates
##          -0.022042567 -0.048848102 -0.069369685 -0.143116735 -0.155979758
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.165286797 -0.174476052 -0.188704348 -0.195619323 -0.220512224
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.226062663 -0.228813899 -0.24113775 -0.277340249 -0.294827343
## alpha              NA           NA          NA           NA           NA
## sigma.sq   0.04805937   0.04805937  0.04805937   0.04805937   0.04805937
##          -0.308103582 -0.311026741 -0.334277933 -0.343935613 -0.356004113
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.358105881 -0.360796274 -0.368734945 -0.391676306 -0.399213836
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.399284019 -0.422514101 -0.434039154 -0.434819003 -0.454790159
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.477252011 -0.488514042 -0.495372826 -0.512363785 -0.525462681
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.528882243 -0.563339519 -0.585182207 -0.61894364 -0.770282542
## alpha              NA           NA           NA          NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937  0.04805937   0.04805937
##          0.042311594 0.051575301 0.053864522 0.388086563 0.399697418
## alpha             NA          NA          NA          NA          NA
## sigma.sq  0.04805937  0.04805937  0.04805937  0.04805937  0.04805937
##          0.404400547 0.476569918 0.539741198 0.822821283 0.845268561
## alpha             NA          NA          NA          NA          NA
## sigma.sq  0.04805937  0.04805937  0.04805937  0.04805937  0.04805937
##          1.092955666 1.698437739  inode3122  inode3123  inode3151
## alpha             NA          NA         NA         NA         NA
## sigma.sq  0.04805937  0.04805937 0.04805937 0.04805937 0.04805937
##           inode3159  inode3160  inode3162  inode3217  inode3218  inode3219
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3238  inode3239  inode3241  inode3242  inode3246  inode3259
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3264  inode3269  inode3272  inode3274  inode3279  inode3280
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3282  inode3284  inode3288  inode3290  inode3297  inode3301
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3315  inode3316  inode3319  inode3326  inode3351  inode3490
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3495  inode3496  inode3501  inode3502  inode3509  inode3513
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3514  inode3525  inode3538  inode3542  inode3572  inode3631
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3714  inode3732  inode3769  inode3970  inode4032  inode4086
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 
## Optima
##          -0.022042567 -0.048848102 -0.069369685 -0.143116735 -0.155979758
## estimate    4.0576335            0            0            0            0
## se          0.7261147            0            0            0            0
##          -0.165286797 -0.174476052 -0.188704348 -0.195619323 -0.220512224
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.226062663 -0.228813899 -0.24113775 -0.277340249 -0.294827343
## estimate            0            0           0            0            0
## se                  0            0           0            0            0
##          -0.308103582 -0.311026741 -0.334277933 -0.343935613 -0.356004113
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.358105881 -0.360796274 -0.368734945 -0.391676306 -0.399213836
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.399284019 -0.422514101 -0.434039154 -0.434819003 -0.454790159
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.477252011 -0.488514042 -0.495372826 -0.512363785 -0.525462681
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.528882243 -0.563339519 -0.585182207 -0.61894364 -0.770282542
## estimate            0            0            0           0            0
## se                  0            0            0           0            0
##          0.042311594 0.051575301 0.053864522 0.388086563 0.399697418
## estimate           0           0           0           0           0
## se                 0           0           0           0           0
##          0.404400547 0.476569918 0.539741198 0.822821283 0.845268561
## estimate           0           0           0           0           0
## se                 0           0           0           0           0
##          1.092955666 1.698437739 inode3122 inode3123 inode3151 inode3159
## estimate           0           0         0         0         0         0
## se                 0           0         0         0         0         0
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate         0         0         0         0         0
## se               0         0         0         0         0
## 
## Arrived at a reliable solution

OU1

OU1_CTL<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OU1_CTL
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 160.2624 160.7624 166.1161   OU1   52
## 
## Rates
##          -0.022042567 -0.048848102 -0.069369685 -0.143116735 -0.155979758
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.165286797 -0.174476052 -0.188704348 -0.195619323 -0.220512224
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.226062663 -0.228813899  -0.24113775 -0.277340249 -0.294827343
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.308103582 -0.311026741 -0.334277933 -0.343935613 -0.356004113
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.358105881 -0.360796274 -0.368734945 -0.391676306 -0.399213836
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.399284019 -0.422514101 -0.434039154 -0.434819003 -0.454790159
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.477252011 -0.488514042 -0.495372826 -0.512363785 -0.525462681
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.528882243 -0.563339519 -0.585182207  -0.61894364 -0.770282542
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           0.042311594  0.051575301  0.053864522  0.388086563  0.399697418
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           0.404400547  0.476569918  0.539741198  0.822821283  0.845268561
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           1.092955666  1.698437739    inode3122    inode3123    inode3151
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3159    inode3160    inode3162    inode3217    inode3218
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3219    inode3238    inode3239    inode3241    inode3242
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3246    inode3259    inode3264    inode3269    inode3272
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3274    inode3279    inode3280    inode3282    inode3284
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3288    inode3290    inode3297    inode3301    inode3315
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3316    inode3319    inode3326    inode3351    inode3490
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3495    inode3496    inode3501    inode3502    inode3509
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3513    inode3514    inode3525    inode3538    inode3542
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3572    inode3631    inode3714    inode3732    inode3769
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3970    inode4032    inode4086
## alpha    2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
## 
## 
## Optima
##          -0.022042567 -0.048848102 -0.069369685 -0.143116735 -0.155979758
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.165286797 -0.174476052 -0.188704348 -0.195619323 -0.220512224
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.226062663 -0.228813899 -0.24113775 -0.277340249 -0.294827343
## estimate    4.0576335    4.0576335   4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536   0.7260536    0.7260536    0.7260536
##          -0.308103582 -0.311026741 -0.334277933 -0.343935613 -0.356004113
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.358105881 -0.360796274 -0.368734945 -0.391676306 -0.399213836
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.399284019 -0.422514101 -0.434039154 -0.434819003 -0.454790159
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.477252011 -0.488514042 -0.495372826 -0.512363785 -0.525462681
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.528882243 -0.563339519 -0.585182207 -0.61894364 -0.770282542
## estimate    4.0576335    4.0576335    4.0576335   4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536   0.7260536    0.7260536
##          0.042311594 0.051575301 0.053864522 0.388086563 0.399697418
## estimate   4.0576335   4.0576335   4.0576335   4.0576335   4.0576335
## se         0.7260536   0.7260536   0.7260536   0.7260536   0.7260536
##          0.404400547 0.476569918 0.539741198 0.822821283 0.845268561
## estimate   4.0576335   4.0576335   4.0576335   4.0576335   4.0576335
## se         0.7260536   0.7260536   0.7260536   0.7260536   0.7260536
##          1.092955666 1.698437739 inode3122 inode3123 inode3151 inode3159
## estimate   4.0576335   4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se         0.7260536   0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 
## 
## Half life (another way of reporting alpha)
## -0.022042567 -0.048848102 -0.069369685 -0.143116735 -0.155979758 
##    308643937    308643937    308643937    308643937    308643937 
## -0.165286797 -0.174476052 -0.188704348 -0.195619323 -0.220512224 
##    308643937    308643937    308643937    308643937    308643937 
## -0.226062663 -0.228813899  -0.24113775 -0.277340249 -0.294827343 
##    308643937    308643937    308643937    308643937    308643937 
## -0.308103582 -0.311026741 -0.334277933 -0.343935613 -0.356004113 
##    308643937    308643937    308643937    308643937    308643937 
## -0.358105881 -0.360796274 -0.368734945 -0.391676306 -0.399213836 
##    308643937    308643937    308643937    308643937    308643937 
## -0.399284019 -0.422514101 -0.434039154 -0.434819003 -0.454790159 
##    308643937    308643937    308643937    308643937    308643937 
## -0.477252011 -0.488514042 -0.495372826 -0.512363785 -0.525462681 
##    308643937    308643937    308643937    308643937    308643937 
## -0.528882243 -0.563339519 -0.585182207  -0.61894364 -0.770282542 
##    308643937    308643937    308643937    308643937    308643937 
##  0.042311594  0.051575301  0.053864522  0.388086563  0.399697418 
##    308643937    308643937    308643937    308643937    308643937 
##  0.404400547  0.476569918  0.539741198  0.822821283  0.845268561 
##    308643937    308643937    308643937    308643937    308643937 
##  1.092955666  1.698437739    inode3122    inode3123    inode3151 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3159    inode3160    inode3162    inode3217    inode3218 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3219    inode3238    inode3239    inode3241    inode3242 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3246    inode3259    inode3264    inode3269    inode3272 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3274    inode3279    inode3280    inode3282    inode3284 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3288    inode3290    inode3297    inode3301    inode3315 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3316    inode3319    inode3326    inode3351    inode3490 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3495    inode3496    inode3501    inode3502    inode3509 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3513    inode3514    inode3525    inode3538    inode3542 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3572    inode3631    inode3714    inode3732    inode3769 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3970    inode4032    inode4086 
##    308643937    308643937    308643937 
## 
## Arrived at a reliable solution
OU1_CTL$eigval
## [1] 2.6e+01 1.3e-06
OU1_CTL$solution.se
##          -0.022042567 -0.048848102 -0.069369685 -0.143116735 -0.155979758
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.165286797 -0.174476052 -0.188704348 -0.195619323 -0.220512224
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.226062663 -0.228813899 -0.24113775 -0.277340249 -0.294827343
## alpha     882.7127566  882.7127566 882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103   0.1961103    0.1961103    0.1961103
##          -0.308103582 -0.311026741 -0.334277933 -0.343935613 -0.356004113
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.358105881 -0.360796274 -0.368734945 -0.391676306 -0.399213836
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.399284019 -0.422514101 -0.434039154 -0.434819003 -0.454790159
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.477252011 -0.488514042 -0.495372826 -0.512363785 -0.525462681
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.528882243 -0.563339519 -0.585182207 -0.61894364 -0.770282542
## alpha     882.7127566  882.7127566  882.7127566 882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103   0.1961103    0.1961103
##          0.042311594 0.051575301 0.053864522 0.388086563 0.399697418
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##          0.404400547 0.476569918 0.539741198 0.822821283 0.845268561
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##          1.092955666 1.698437739   inode3122   inode3123   inode3151
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3159   inode3160   inode3162   inode3217   inode3218
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3219   inode3238   inode3239   inode3241   inode3242
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3246   inode3259   inode3264   inode3269   inode3272
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3274   inode3279   inode3280   inode3282   inode3284
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3288   inode3290   inode3297   inode3301   inode3315
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3316   inode3319   inode3326   inode3351   inode3490
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3495   inode3496   inode3501   inode3502   inode3509
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3513   inode3514   inode3525   inode3538   inode3542
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3572   inode3631   inode3714   inode3732   inode3769
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3970   inode4032   inode4086
## alpha    882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103

OUM

OUM_CTL<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OUM_CTL
## 
## Fit
##       lnL       AIC     AICc       BIC model ntax
##  85.24088 -152.4818 -148.196 -134.9206   OUM   52
## 
## 
## Rates
##                   1          2          3          4          5          6
## alpha    5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
##                   7
## alpha    5.78373949
## sigma.sq 0.02552326
## 
## Optima
##                   1          2          3          4          5          6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se       0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
##                   7
## estimate 6.99998674
## se       0.01485411
## 
## 
## Half life (another way of reporting alpha)
##         1         2         3         4         5         6         7 
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 
## 
## Arrived at a reliable solution

AIC

aic<-setNames(c(BM1_CTL$AICc,OU1_CTL$AICc,OUM_CTL$AICc),
              c("BM","OU1","OUM"))
aic
##        BM       OU1       OUM 
##  158.5073  160.7624 -148.1960
aic.w(aic)
##  BM OU1 OUM 
##   0   0   1

GF

dat<-read.csv("./data/Ouwie_data/GF_OUwie_ManyOptions_optima.csv")

BM

BM1_GF<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
BM1_GF
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 158.2624 158.5073 162.1649   BM1   52
## 
## Rates
##          -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## alpha              NA           NA           NA           NA          NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937  0.04805937
##          -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## alpha              NA           NA           NA          NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937  0.04805937   0.04805937
##          -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          0.079914355 1.349473949  inode3122  inode3123  inode3151
## alpha             NA          NA         NA         NA         NA
## sigma.sq  0.04805937  0.04805937 0.04805937 0.04805937 0.04805937
##           inode3159  inode3160  inode3162  inode3217  inode3218  inode3219
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3238  inode3239  inode3241  inode3242  inode3246  inode3259
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3264  inode3269  inode3272  inode3274  inode3279  inode3280
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3282  inode3284  inode3288  inode3290  inode3297  inode3301
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3315  inode3316  inode3319  inode3326  inode3351  inode3490
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3495  inode3496  inode3501  inode3502  inode3509  inode3513
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3514  inode3525  inode3538  inode3542  inode3572  inode3631
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3714  inode3732  inode3769  inode3970  inode4032  inode4086
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 
## Optima
##          -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## estimate    4.0576335            0            0            0            0
## se          0.7261147            0            0            0            0
##          -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## estimate            0            0            0            0           0
## se                  0            0            0            0           0
##          -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## estimate            0            0            0           0            0
## se                  0            0            0           0            0
##          -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          0.079914355 1.349473949 inode3122 inode3123 inode3151 inode3159
## estimate           0           0         0         0         0         0
## se                 0           0         0         0         0         0
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate         0         0         0         0         0
## se               0         0         0         0         0
## 
## Arrived at a reliable solution

OU1

OU1_GF<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OU1_GF
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 160.2624 160.7624 166.1161   OU1   52
## 
## Rates
##          -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.409662437 -0.419808798 -0.423308801 -0.425565648  -0.42583897
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.438880858 -0.448896787 -0.454790159  -0.45813357 -0.460589809
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           0.079914355  1.349473949    inode3122    inode3123    inode3151
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3159    inode3160    inode3162    inode3217    inode3218
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3219    inode3238    inode3239    inode3241    inode3242
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3246    inode3259    inode3264    inode3269    inode3272
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3274    inode3279    inode3280    inode3282    inode3284
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3288    inode3290    inode3297    inode3301    inode3315
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3316    inode3319    inode3326    inode3351    inode3490
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3495    inode3496    inode3501    inode3502    inode3509
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3513    inode3514    inode3525    inode3538    inode3542
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3572    inode3631    inode3714    inode3732    inode3769
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3970    inode4032    inode4086
## alpha    2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
## 
## 
## Optima
##          -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## estimate    4.0576335    4.0576335    4.0576335    4.0576335   4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536   0.7260536
##          -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## estimate    4.0576335    4.0576335    4.0576335   4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536   0.7260536    0.7260536
##          -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          0.079914355 1.349473949 inode3122 inode3123 inode3151 inode3159
## estimate   4.0576335   4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se         0.7260536   0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 
## 
## Half life (another way of reporting alpha)
## -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123 
##    308643937    308643937    308643937    308643937    308643937 
## -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169 
##    308643937    308643937    308643937    308643937    308643937 
## -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302 
##    308643937    308643937    308643937    308643937    308643937 
## -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486 
##    308643937    308643937    308643937    308643937    308643937 
## -0.409662437 -0.419808798 -0.423308801 -0.425565648  -0.42583897 
##    308643937    308643937    308643937    308643937    308643937 
## -0.438880858 -0.448896787 -0.454790159  -0.45813357 -0.460589809 
##    308643937    308643937    308643937    308643937    308643937 
## -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314 
##    308643937    308643937    308643937    308643937    308643937 
## -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591 
##    308643937    308643937    308643937    308643937    308643937 
## -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762 
##    308643937    308643937    308643937    308643937    308643937 
## -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872 
##    308643937    308643937    308643937    308643937    308643937 
##  0.079914355  1.349473949    inode3122    inode3123    inode3151 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3159    inode3160    inode3162    inode3217    inode3218 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3219    inode3238    inode3239    inode3241    inode3242 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3246    inode3259    inode3264    inode3269    inode3272 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3274    inode3279    inode3280    inode3282    inode3284 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3288    inode3290    inode3297    inode3301    inode3315 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3316    inode3319    inode3326    inode3351    inode3490 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3495    inode3496    inode3501    inode3502    inode3509 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3513    inode3514    inode3525    inode3538    inode3542 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3572    inode3631    inode3714    inode3732    inode3769 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3970    inode4032    inode4086 
##    308643937    308643937    308643937 
## 
## Arrived at a reliable solution
OU1_GF$eigval
## [1] 2.6e+01 1.3e-06
OU1_GF$solution.se
##          -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## alpha     882.7127566  882.7127566  882.7127566  882.7127566 882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103   0.1961103
##          -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## alpha     882.7127566  882.7127566  882.7127566 882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103   0.1961103    0.1961103
##          -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          0.079914355 1.349473949   inode3122   inode3123   inode3151
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3159   inode3160   inode3162   inode3217   inode3218
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3219   inode3238   inode3239   inode3241   inode3242
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3246   inode3259   inode3264   inode3269   inode3272
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3274   inode3279   inode3280   inode3282   inode3284
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3288   inode3290   inode3297   inode3301   inode3315
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3316   inode3319   inode3326   inode3351   inode3490
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3495   inode3496   inode3501   inode3502   inode3509
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3513   inode3514   inode3525   inode3538   inode3542
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3572   inode3631   inode3714   inode3732   inode3769
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3970   inode4032   inode4086
## alpha    882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103

OUM

OUM_GF<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OUM_GF
## 
## Fit
##       lnL       AIC     AICc       BIC model ntax
##  85.24088 -152.4818 -148.196 -134.9206   OUM   52
## 
## 
## Rates
##                   1          2          3          4          5          6
## alpha    5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
##                   7
## alpha    5.78373949
## sigma.sq 0.02552326
## 
## Optima
##                   1          2          3          4          5          6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se       0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
##                   7
## estimate 6.99998674
## se       0.01485411
## 
## 
## Half life (another way of reporting alpha)
##         1         2         3         4         5         6         7 
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 
## 
## Arrived at a reliable solution

AIC

aic<-setNames(c(BM1_GF$AICc,OU1_GF$AICc,OUM_GF$AICc),
              c("BM","OU1","OUM"))
aic
##        BM       OU1       OUM 
##  158.5073  160.7624 -148.1960
aic.w(aic)
##  BM OU1 OUM 
##   0   0   1

BPP

dat<-read.csv("./data/Ouwie_data/BPP_OUwie_ManyOptions_optima.csv")

BM

BM1_BPP<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
BM1_BPP
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 158.2624 158.5073 162.1649   BM1   52
## 
## Rates
##          -0.105145425 -0.119084599 -0.188704348 -0.225036539 -0.255317351
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.30627187 -0.327981232 -0.334277933 -0.343935613 -0.347029762
## alpha             NA           NA           NA           NA           NA
## sigma.sq  0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.359161832 -0.359945235 -0.368913567 -0.380235729 -0.398461713
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.399213836 -0.399284019 -0.408989879 -0.428224485 -0.442200811
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.447400078 -0.449261397 -0.454790159 -0.466734078 -0.467614451
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.471618177 -0.473209269 -0.483120435 -0.494906486 -0.496293077
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.563339519 -0.579918045 -0.581015956 -0.60291507 -0.612242656
## alpha              NA           NA           NA          NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937  0.04805937   0.04805937
##          -0.61894364 -0.652729444 -0.731309262 0.117400503 0.12862613
## alpha             NA           NA           NA          NA         NA
## sigma.sq  0.04805937   0.04805937   0.04805937  0.04805937 0.04805937
##          0.447183364 0.510616761 0.519681634 0.627037582 0.788405152
## alpha             NA          NA          NA          NA          NA
## sigma.sq  0.04805937  0.04805937  0.04805937  0.04805937  0.04805937
##          1.035253997 1.041012607 1.118621879 1.397025289 1.453249541
## alpha             NA          NA          NA          NA          NA
## sigma.sq  0.04805937  0.04805937  0.04805937  0.04805937  0.04805937
##          1.463514021 2.829425593  inode3122  inode3123  inode3151
## alpha             NA          NA         NA         NA         NA
## sigma.sq  0.04805937  0.04805937 0.04805937 0.04805937 0.04805937
##           inode3159  inode3160  inode3162  inode3217  inode3218  inode3219
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3238  inode3239  inode3241  inode3242  inode3246  inode3259
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3264  inode3269  inode3272  inode3274  inode3279  inode3280
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3282  inode3284  inode3288  inode3290  inode3297  inode3301
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3315  inode3316  inode3319  inode3326  inode3351  inode3490
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3495  inode3496  inode3501  inode3502  inode3509  inode3513
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3514  inode3525  inode3538  inode3542  inode3572  inode3631
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3714  inode3732  inode3769  inode3970  inode4032  inode4086
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 
## Optima
##          -0.105145425 -0.119084599 -0.188704348 -0.225036539 -0.255317351
## estimate    4.0576335            0            0            0            0
## se          0.7261147            0            0            0            0
##          -0.30627187 -0.327981232 -0.334277933 -0.343935613 -0.347029762
## estimate           0            0            0            0            0
## se                 0            0            0            0            0
##          -0.359161832 -0.359945235 -0.368913567 -0.380235729 -0.398461713
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.399213836 -0.399284019 -0.408989879 -0.428224485 -0.442200811
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.447400078 -0.449261397 -0.454790159 -0.466734078 -0.467614451
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.471618177 -0.473209269 -0.483120435 -0.494906486 -0.496293077
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.563339519 -0.579918045 -0.581015956 -0.60291507 -0.612242656
## estimate            0            0            0           0            0
## se                  0            0            0           0            0
##          -0.61894364 -0.652729444 -0.731309262 0.117400503 0.12862613
## estimate           0            0            0           0          0
## se                 0            0            0           0          0
##          0.447183364 0.510616761 0.519681634 0.627037582 0.788405152
## estimate           0           0           0           0           0
## se                 0           0           0           0           0
##          1.035253997 1.041012607 1.118621879 1.397025289 1.453249541
## estimate           0           0           0           0           0
## se                 0           0           0           0           0
##          1.463514021 2.829425593 inode3122 inode3123 inode3151 inode3159
## estimate           0           0         0         0         0         0
## se                 0           0         0         0         0         0
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate         0         0         0         0         0
## se               0         0         0         0         0
## 
## Arrived at a reliable solution

OU1

OU1_BPP<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OU1_BPP
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 160.2624 160.7624 166.1161   OU1   52
## 
## Rates
##          -0.105145425 -0.119084599 -0.188704348 -0.225036539 -0.255317351
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           -0.30627187 -0.327981232 -0.334277933 -0.343935613 -0.347029762
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.359161832 -0.359945235 -0.368913567 -0.380235729 -0.398461713
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.399213836 -0.399284019 -0.408989879 -0.428224485 -0.442200811
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.447400078 -0.449261397 -0.454790159 -0.466734078 -0.467614451
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.471618177 -0.473209269 -0.483120435 -0.494906486 -0.496293077
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.563339519 -0.579918045 -0.581015956  -0.60291507 -0.612242656
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           -0.61894364 -0.652729444 -0.731309262  0.117400503   0.12862613
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           0.447183364  0.510616761  0.519681634  0.627037582  0.788405152
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           1.035253997  1.041012607  1.118621879  1.397025289  1.453249541
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           1.463514021  2.829425593    inode3122    inode3123    inode3151
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3159    inode3160    inode3162    inode3217    inode3218
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3219    inode3238    inode3239    inode3241    inode3242
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3246    inode3259    inode3264    inode3269    inode3272
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3274    inode3279    inode3280    inode3282    inode3284
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3288    inode3290    inode3297    inode3301    inode3315
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3316    inode3319    inode3326    inode3351    inode3490
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3495    inode3496    inode3501    inode3502    inode3509
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3513    inode3514    inode3525    inode3538    inode3542
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3572    inode3631    inode3714    inode3732    inode3769
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3970    inode4032    inode4086
## alpha    2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
## 
## 
## Optima
##          -0.105145425 -0.119084599 -0.188704348 -0.225036539 -0.255317351
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.30627187 -0.327981232 -0.334277933 -0.343935613 -0.347029762
## estimate   4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se         0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.359161832 -0.359945235 -0.368913567 -0.380235729 -0.398461713
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.399213836 -0.399284019 -0.408989879 -0.428224485 -0.442200811
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.447400078 -0.449261397 -0.454790159 -0.466734078 -0.467614451
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.471618177 -0.473209269 -0.483120435 -0.494906486 -0.496293077
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.563339519 -0.579918045 -0.581015956 -0.60291507 -0.612242656
## estimate    4.0576335    4.0576335    4.0576335   4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536   0.7260536    0.7260536
##          -0.61894364 -0.652729444 -0.731309262 0.117400503 0.12862613
## estimate   4.0576335    4.0576335    4.0576335   4.0576335  4.0576335
## se         0.7260536    0.7260536    0.7260536   0.7260536  0.7260536
##          0.447183364 0.510616761 0.519681634 0.627037582 0.788405152
## estimate   4.0576335   4.0576335   4.0576335   4.0576335   4.0576335
## se         0.7260536   0.7260536   0.7260536   0.7260536   0.7260536
##          1.035253997 1.041012607 1.118621879 1.397025289 1.453249541
## estimate   4.0576335   4.0576335   4.0576335   4.0576335   4.0576335
## se         0.7260536   0.7260536   0.7260536   0.7260536   0.7260536
##          1.463514021 2.829425593 inode3122 inode3123 inode3151 inode3159
## estimate   4.0576335   4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se         0.7260536   0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 
## 
## Half life (another way of reporting alpha)
## -0.105145425 -0.119084599 -0.188704348 -0.225036539 -0.255317351 
##    308643937    308643937    308643937    308643937    308643937 
##  -0.30627187 -0.327981232 -0.334277933 -0.343935613 -0.347029762 
##    308643937    308643937    308643937    308643937    308643937 
## -0.359161832 -0.359945235 -0.368913567 -0.380235729 -0.398461713 
##    308643937    308643937    308643937    308643937    308643937 
## -0.399213836 -0.399284019 -0.408989879 -0.428224485 -0.442200811 
##    308643937    308643937    308643937    308643937    308643937 
## -0.447400078 -0.449261397 -0.454790159 -0.466734078 -0.467614451 
##    308643937    308643937    308643937    308643937    308643937 
## -0.471618177 -0.473209269 -0.483120435 -0.494906486 -0.496293077 
##    308643937    308643937    308643937    308643937    308643937 
## -0.563339519 -0.579918045 -0.581015956  -0.60291507 -0.612242656 
##    308643937    308643937    308643937    308643937    308643937 
##  -0.61894364 -0.652729444 -0.731309262  0.117400503   0.12862613 
##    308643937    308643937    308643937    308643937    308643937 
##  0.447183364  0.510616761  0.519681634  0.627037582  0.788405152 
##    308643937    308643937    308643937    308643937    308643937 
##  1.035253997  1.041012607  1.118621879  1.397025289  1.453249541 
##    308643937    308643937    308643937    308643937    308643937 
##  1.463514021  2.829425593    inode3122    inode3123    inode3151 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3159    inode3160    inode3162    inode3217    inode3218 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3219    inode3238    inode3239    inode3241    inode3242 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3246    inode3259    inode3264    inode3269    inode3272 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3274    inode3279    inode3280    inode3282    inode3284 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3288    inode3290    inode3297    inode3301    inode3315 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3316    inode3319    inode3326    inode3351    inode3490 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3495    inode3496    inode3501    inode3502    inode3509 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3513    inode3514    inode3525    inode3538    inode3542 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3572    inode3631    inode3714    inode3732    inode3769 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3970    inode4032    inode4086 
##    308643937    308643937    308643937 
## 
## Arrived at a reliable solution
OU1_BPP$eigval
## [1] 2.6e+01 1.3e-06
OU1_BPP$solution.se
##          -0.105145425 -0.119084599 -0.188704348 -0.225036539 -0.255317351
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.30627187 -0.327981232 -0.334277933 -0.343935613 -0.347029762
## alpha    882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq   0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.359161832 -0.359945235 -0.368913567 -0.380235729 -0.398461713
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.399213836 -0.399284019 -0.408989879 -0.428224485 -0.442200811
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.447400078 -0.449261397 -0.454790159 -0.466734078 -0.467614451
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.471618177 -0.473209269 -0.483120435 -0.494906486 -0.496293077
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.563339519 -0.579918045 -0.581015956 -0.60291507 -0.612242656
## alpha     882.7127566  882.7127566  882.7127566 882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103   0.1961103    0.1961103
##          -0.61894364 -0.652729444 -0.731309262 0.117400503  0.12862613
## alpha    882.7127566  882.7127566  882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103    0.1961103    0.1961103   0.1961103   0.1961103
##          0.447183364 0.510616761 0.519681634 0.627037582 0.788405152
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##          1.035253997 1.041012607 1.118621879 1.397025289 1.453249541
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##          1.463514021 2.829425593   inode3122   inode3123   inode3151
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3159   inode3160   inode3162   inode3217   inode3218
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3219   inode3238   inode3239   inode3241   inode3242
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3246   inode3259   inode3264   inode3269   inode3272
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3274   inode3279   inode3280   inode3282   inode3284
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3288   inode3290   inode3297   inode3301   inode3315
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3316   inode3319   inode3326   inode3351   inode3490
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3495   inode3496   inode3501   inode3502   inode3509
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3513   inode3514   inode3525   inode3538   inode3542
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3572   inode3631   inode3714   inode3732   inode3769
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3970   inode4032   inode4086
## alpha    882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103

OUM

OUM_BPP<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OUM_BPP
## 
## Fit
##       lnL       AIC     AICc       BIC model ntax
##  85.24088 -152.4818 -148.196 -134.9206   OUM   52
## 
## 
## Rates
##                   1          2          3          4          5          6
## alpha    5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
##                   7
## alpha    5.78373949
## sigma.sq 0.02552326
## 
## Optima
##                   1          2          3          4          5          6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se       0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
##                   7
## estimate 6.99998674
## se       0.01485411
## 
## 
## Half life (another way of reporting alpha)
##         1         2         3         4         5         6         7 
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 
## 
## Arrived at a reliable solution

AIC

aic<-setNames(c(BM1_BPP$AICc,OU1_BPP$AICc,OUM_BPP$AICc),
              c("BM","OU1","OUM"))
aic
##        BM       OU1       OUM 
##  158.5073  160.7624 -148.1960
aic.w(aic)
##  BM OU1 OUM 
##   0   0   1

LAAO

dat<-read.csv("./data/Ouwie_data/LAAO_OUwie_ManyOptions_optima.csv")

BM

BM1_LAAO<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
BM1_LAAO
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 158.2624 158.5073 162.1649   BM1   52
## 
## Rates
##          -0.092648244 -0.100295794 -0.128998329 -0.21620634 -0.230245425
## alpha              NA           NA           NA          NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937  0.04805937   0.04805937
##          -0.239964336 -0.257771998 -0.258593859 -0.270929154 -0.291282471
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.318364164 -0.324668291 -0.334277933 -0.337841517 -0.343571052
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.343935613 -0.347029762 -0.348104493 -0.359161832 -0.372459947
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.376103195 -0.378251319 -0.399213836 -0.399284019 -0.402697024
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.404809885 -0.408989879 -0.409571651 -0.410097725 -0.411566673
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.422109758 -0.423308801 -0.423417345 -0.424255936 -0.430927124
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.442200811 -0.454790159 -0.459411318 -0.463327573 -0.463654083
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.478165354 -0.486637693 -0.505966472 -0.539435104 -0.555961591
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.563339519 -0.585142053 -0.612242656 -0.646133988 -0.723025233
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          0.011750916 0.019517693  inode3122  inode3123  inode3151
## alpha             NA          NA         NA         NA         NA
## sigma.sq  0.04805937  0.04805937 0.04805937 0.04805937 0.04805937
##           inode3159  inode3160  inode3162  inode3217  inode3218  inode3219
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3238  inode3239  inode3241  inode3242  inode3246  inode3259
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3264  inode3269  inode3272  inode3274  inode3279  inode3280
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3282  inode3284  inode3288  inode3290  inode3297  inode3301
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3315  inode3316  inode3319  inode3326  inode3351  inode3490
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3495  inode3496  inode3501  inode3502  inode3509  inode3513
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3514  inode3525  inode3538  inode3542  inode3572  inode3631
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3714  inode3732  inode3769  inode3970  inode4032  inode4086
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 
## Optima
##          -0.092648244 -0.100295794 -0.128998329 -0.21620634 -0.230245425
## estimate    4.0576335            0            0           0            0
## se          0.7261147            0            0           0            0
##          -0.239964336 -0.257771998 -0.258593859 -0.270929154 -0.291282471
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.318364164 -0.324668291 -0.334277933 -0.337841517 -0.343571052
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.343935613 -0.347029762 -0.348104493 -0.359161832 -0.372459947
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.376103195 -0.378251319 -0.399213836 -0.399284019 -0.402697024
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.404809885 -0.408989879 -0.409571651 -0.410097725 -0.411566673
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.422109758 -0.423308801 -0.423417345 -0.424255936 -0.430927124
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.442200811 -0.454790159 -0.459411318 -0.463327573 -0.463654083
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.478165354 -0.486637693 -0.505966472 -0.539435104 -0.555961591
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.563339519 -0.585142053 -0.612242656 -0.646133988 -0.723025233
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          0.011750916 0.019517693 inode3122 inode3123 inode3151 inode3159
## estimate           0           0         0         0         0         0
## se                 0           0         0         0         0         0
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate         0         0         0         0         0
## se               0         0         0         0         0
## 
## Arrived at a reliable solution

OU1

OU1_LAAO<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OU1_LAAO
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 160.2624 160.7624 166.1161   OU1   52
## 
## Rates
##          -0.092648244 -0.100295794 -0.128998329  -0.21620634 -0.230245425
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.239964336 -0.257771998 -0.258593859 -0.270929154 -0.291282471
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.318364164 -0.324668291 -0.334277933 -0.337841517 -0.343571052
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.343935613 -0.347029762 -0.348104493 -0.359161832 -0.372459947
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.376103195 -0.378251319 -0.399213836 -0.399284019 -0.402697024
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.404809885 -0.408989879 -0.409571651 -0.410097725 -0.411566673
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.422109758 -0.423308801 -0.423417345 -0.424255936 -0.430927124
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.442200811 -0.454790159 -0.459411318 -0.463327573 -0.463654083
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.478165354 -0.486637693 -0.505966472 -0.539435104 -0.555961591
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.563339519 -0.585142053 -0.612242656 -0.646133988 -0.723025233
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           0.011750916  0.019517693    inode3122    inode3123    inode3151
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3159    inode3160    inode3162    inode3217    inode3218
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3219    inode3238    inode3239    inode3241    inode3242
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3246    inode3259    inode3264    inode3269    inode3272
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3274    inode3279    inode3280    inode3282    inode3284
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3288    inode3290    inode3297    inode3301    inode3315
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3316    inode3319    inode3326    inode3351    inode3490
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3495    inode3496    inode3501    inode3502    inode3509
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3513    inode3514    inode3525    inode3538    inode3542
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3572    inode3631    inode3714    inode3732    inode3769
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3970    inode4032    inode4086
## alpha    2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
## 
## 
## Optima
##          -0.092648244 -0.100295794 -0.128998329 -0.21620634 -0.230245425
## estimate    4.0576335    4.0576335    4.0576335   4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536   0.7260536    0.7260536
##          -0.239964336 -0.257771998 -0.258593859 -0.270929154 -0.291282471
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.318364164 -0.324668291 -0.334277933 -0.337841517 -0.343571052
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.343935613 -0.347029762 -0.348104493 -0.359161832 -0.372459947
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.376103195 -0.378251319 -0.399213836 -0.399284019 -0.402697024
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.404809885 -0.408989879 -0.409571651 -0.410097725 -0.411566673
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.422109758 -0.423308801 -0.423417345 -0.424255936 -0.430927124
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.442200811 -0.454790159 -0.459411318 -0.463327573 -0.463654083
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.478165354 -0.486637693 -0.505966472 -0.539435104 -0.555961591
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.563339519 -0.585142053 -0.612242656 -0.646133988 -0.723025233
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          0.011750916 0.019517693 inode3122 inode3123 inode3151 inode3159
## estimate   4.0576335   4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se         0.7260536   0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 
## 
## Half life (another way of reporting alpha)
## -0.092648244 -0.100295794 -0.128998329  -0.21620634 -0.230245425 
##    308643937    308643937    308643937    308643937    308643937 
## -0.239964336 -0.257771998 -0.258593859 -0.270929154 -0.291282471 
##    308643937    308643937    308643937    308643937    308643937 
## -0.318364164 -0.324668291 -0.334277933 -0.337841517 -0.343571052 
##    308643937    308643937    308643937    308643937    308643937 
## -0.343935613 -0.347029762 -0.348104493 -0.359161832 -0.372459947 
##    308643937    308643937    308643937    308643937    308643937 
## -0.376103195 -0.378251319 -0.399213836 -0.399284019 -0.402697024 
##    308643937    308643937    308643937    308643937    308643937 
## -0.404809885 -0.408989879 -0.409571651 -0.410097725 -0.411566673 
##    308643937    308643937    308643937    308643937    308643937 
## -0.422109758 -0.423308801 -0.423417345 -0.424255936 -0.430927124 
##    308643937    308643937    308643937    308643937    308643937 
## -0.442200811 -0.454790159 -0.459411318 -0.463327573 -0.463654083 
##    308643937    308643937    308643937    308643937    308643937 
## -0.478165354 -0.486637693 -0.505966472 -0.539435104 -0.555961591 
##    308643937    308643937    308643937    308643937    308643937 
## -0.563339519 -0.585142053 -0.612242656 -0.646133988 -0.723025233 
##    308643937    308643937    308643937    308643937    308643937 
##  0.011750916  0.019517693    inode3122    inode3123    inode3151 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3159    inode3160    inode3162    inode3217    inode3218 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3219    inode3238    inode3239    inode3241    inode3242 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3246    inode3259    inode3264    inode3269    inode3272 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3274    inode3279    inode3280    inode3282    inode3284 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3288    inode3290    inode3297    inode3301    inode3315 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3316    inode3319    inode3326    inode3351    inode3490 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3495    inode3496    inode3501    inode3502    inode3509 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3513    inode3514    inode3525    inode3538    inode3542 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3572    inode3631    inode3714    inode3732    inode3769 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3970    inode4032    inode4086 
##    308643937    308643937    308643937 
## 
## Arrived at a reliable solution
OU1_LAAO$eigval
## [1] 2.6e+01 1.3e-06
OU1_LAAO$solution.se
##          -0.092648244 -0.100295794 -0.128998329 -0.21620634 -0.230245425
## alpha     882.7127566  882.7127566  882.7127566 882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103   0.1961103    0.1961103
##          -0.239964336 -0.257771998 -0.258593859 -0.270929154 -0.291282471
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.318364164 -0.324668291 -0.334277933 -0.337841517 -0.343571052
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.343935613 -0.347029762 -0.348104493 -0.359161832 -0.372459947
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.376103195 -0.378251319 -0.399213836 -0.399284019 -0.402697024
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.404809885 -0.408989879 -0.409571651 -0.410097725 -0.411566673
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.422109758 -0.423308801 -0.423417345 -0.424255936 -0.430927124
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.442200811 -0.454790159 -0.459411318 -0.463327573 -0.463654083
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.478165354 -0.486637693 -0.505966472 -0.539435104 -0.555961591
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.563339519 -0.585142053 -0.612242656 -0.646133988 -0.723025233
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          0.011750916 0.019517693   inode3122   inode3123   inode3151
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3159   inode3160   inode3162   inode3217   inode3218
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3219   inode3238   inode3239   inode3241   inode3242
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3246   inode3259   inode3264   inode3269   inode3272
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3274   inode3279   inode3280   inode3282   inode3284
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3288   inode3290   inode3297   inode3301   inode3315
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3316   inode3319   inode3326   inode3351   inode3490
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3495   inode3496   inode3501   inode3502   inode3509
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3513   inode3514   inode3525   inode3538   inode3542
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3572   inode3631   inode3714   inode3732   inode3769
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3970   inode4032   inode4086
## alpha    882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103

OUM

OUM_LAAO<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OUM_LAAO
## 
## Fit
##       lnL       AIC     AICc       BIC model ntax
##  85.24088 -152.4818 -148.196 -134.9206   OUM   52
## 
## 
## Rates
##                   1          2          3          4          5          6
## alpha    5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
##                   7
## alpha    5.78373949
## sigma.sq 0.02552326
## 
## Optima
##                   1          2          3          4          5          6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se       0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
##                   7
## estimate 6.99998674
## se       0.01485411
## 
## 
## Half life (another way of reporting alpha)
##         1         2         3         4         5         6         7 
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 
## 
## Arrived at a reliable solution

AIC

aic<-setNames(c(BM1_LAAO$AICc,OU1_LAAO$AICc,OUM_LAAO$AICc),
              c("BM","OU1","OUM"))
aic
##        BM       OU1       OUM 
##  158.5073  160.7624 -148.1960
aic.w(aic)
##  BM OU1 OUM 
##   0   0   1

KSPI

dat<-read.csv("./data/Ouwie_data/KSPI_OUwie_ManyOptions_optima.csv")

BM

BM1_KSPI<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
BM1_KSPI
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 158.2624 158.5073 162.1649   BM1   52
## 
## Rates
##          -0.115762862 -0.218459259 -0.276269351 -0.324668291 -0.334277933
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.343935613 -0.347029762 -0.36429282 -0.36971411 -0.376347838
## alpha              NA           NA          NA          NA           NA
## sigma.sq   0.04805937   0.04805937  0.04805937  0.04805937   0.04805937
##          -0.395173036 -0.399213836 -0.399284019 -0.40249729 -0.419749836
## alpha              NA           NA           NA          NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937  0.04805937   0.04805937
##          -0.422992017 -0.449261397 -0.451042648 -0.454790159 -0.4580531
## alpha              NA           NA           NA           NA         NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937 0.04805937
##          -0.458694297 -0.461032003 -0.466734078 -0.478411682 -0.494906486
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.496224454 -0.507701406 -0.52278517 -0.527324428 -0.527913521
## alpha              NA           NA          NA           NA           NA
## sigma.sq   0.04805937   0.04805937  0.04805937   0.04805937   0.04805937
##          -0.535408592 -0.539435104 -0.548287973 -0.555961591 -0.569277353
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.580540919 -0.581015956 -0.600904674 -0.651365854 -0.665162495
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.684832772 -0.69527236 -0.709372748 -0.731309262 -0.779848299
## alpha              NA          NA           NA           NA           NA
## sigma.sq   0.04805937  0.04805937   0.04805937   0.04805937   0.04805937
##          -0.825512855 -0.874226881 -0.96572225 0.042118192 0.173328997
## alpha              NA           NA          NA          NA          NA
## sigma.sq   0.04805937   0.04805937  0.04805937  0.04805937  0.04805937
##          0.867471889 2.30436465  inode3122  inode3123  inode3151
## alpha             NA         NA         NA         NA         NA
## sigma.sq  0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3159  inode3160  inode3162  inode3217  inode3218  inode3219
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3238  inode3239  inode3241  inode3242  inode3246  inode3259
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3264  inode3269  inode3272  inode3274  inode3279  inode3280
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3282  inode3284  inode3288  inode3290  inode3297  inode3301
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3315  inode3316  inode3319  inode3326  inode3351  inode3490
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3495  inode3496  inode3501  inode3502  inode3509  inode3513
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3514  inode3525  inode3538  inode3542  inode3572  inode3631
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3714  inode3732  inode3769  inode3970  inode4032  inode4086
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 
## Optima
##          -0.115762862 -0.218459259 -0.276269351 -0.324668291 -0.334277933
## estimate    4.0576335            0            0            0            0
## se          0.7261147            0            0            0            0
##          -0.343935613 -0.347029762 -0.36429282 -0.36971411 -0.376347838
## estimate            0            0           0           0            0
## se                  0            0           0           0            0
##          -0.395173036 -0.399213836 -0.399284019 -0.40249729 -0.419749836
## estimate            0            0            0           0            0
## se                  0            0            0           0            0
##          -0.422992017 -0.449261397 -0.451042648 -0.454790159 -0.4580531
## estimate            0            0            0            0          0
## se                  0            0            0            0          0
##          -0.458694297 -0.461032003 -0.466734078 -0.478411682 -0.494906486
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.496224454 -0.507701406 -0.52278517 -0.527324428 -0.527913521
## estimate            0            0           0            0            0
## se                  0            0           0            0            0
##          -0.535408592 -0.539435104 -0.548287973 -0.555961591 -0.569277353
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.580540919 -0.581015956 -0.600904674 -0.651365854 -0.665162495
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.684832772 -0.69527236 -0.709372748 -0.731309262 -0.779848299
## estimate            0           0            0            0            0
## se                  0           0            0            0            0
##          -0.825512855 -0.874226881 -0.96572225 0.042118192 0.173328997
## estimate            0            0           0           0           0
## se                  0            0           0           0           0
##          0.867471889 2.30436465 inode3122 inode3123 inode3151 inode3159
## estimate           0          0         0         0         0         0
## se                 0          0         0         0         0         0
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate         0         0         0         0         0
## se               0         0         0         0         0
## 
## Arrived at a reliable solution

OU1

OU1_KSPI<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OU1_KSPI
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 160.2624 160.7624 166.1161   OU1   52
## 
## Rates
##          -0.115762862 -0.218459259 -0.276269351 -0.324668291 -0.334277933
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.343935613 -0.347029762  -0.36429282  -0.36971411 -0.376347838
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.395173036 -0.399213836 -0.399284019  -0.40249729 -0.419749836
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.422992017 -0.449261397 -0.451042648 -0.454790159   -0.4580531
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.458694297 -0.461032003 -0.466734078 -0.478411682 -0.494906486
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.496224454 -0.507701406  -0.52278517 -0.527324428 -0.527913521
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.535408592 -0.539435104 -0.548287973 -0.555961591 -0.569277353
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.580540919 -0.581015956 -0.600904674 -0.651365854 -0.665162495
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.684832772  -0.69527236 -0.709372748 -0.731309262 -0.779848299
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.825512855 -0.874226881  -0.96572225  0.042118192  0.173328997
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           0.867471889   2.30436465    inode3122    inode3123    inode3151
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3159    inode3160    inode3162    inode3217    inode3218
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3219    inode3238    inode3239    inode3241    inode3242
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3246    inode3259    inode3264    inode3269    inode3272
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3274    inode3279    inode3280    inode3282    inode3284
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3288    inode3290    inode3297    inode3301    inode3315
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3316    inode3319    inode3326    inode3351    inode3490
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3495    inode3496    inode3501    inode3502    inode3509
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3513    inode3514    inode3525    inode3538    inode3542
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3572    inode3631    inode3714    inode3732    inode3769
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3970    inode4032    inode4086
## alpha    2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
## 
## 
## Optima
##          -0.115762862 -0.218459259 -0.276269351 -0.324668291 -0.334277933
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.343935613 -0.347029762 -0.36429282 -0.36971411 -0.376347838
## estimate    4.0576335    4.0576335   4.0576335   4.0576335    4.0576335
## se          0.7260536    0.7260536   0.7260536   0.7260536    0.7260536
##          -0.395173036 -0.399213836 -0.399284019 -0.40249729 -0.419749836
## estimate    4.0576335    4.0576335    4.0576335   4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536   0.7260536    0.7260536
##          -0.422992017 -0.449261397 -0.451042648 -0.454790159 -0.4580531
## estimate    4.0576335    4.0576335    4.0576335    4.0576335  4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536  0.7260536
##          -0.458694297 -0.461032003 -0.466734078 -0.478411682 -0.494906486
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.496224454 -0.507701406 -0.52278517 -0.527324428 -0.527913521
## estimate    4.0576335    4.0576335   4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536   0.7260536    0.7260536    0.7260536
##          -0.535408592 -0.539435104 -0.548287973 -0.555961591 -0.569277353
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.580540919 -0.581015956 -0.600904674 -0.651365854 -0.665162495
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.684832772 -0.69527236 -0.709372748 -0.731309262 -0.779848299
## estimate    4.0576335   4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536   0.7260536    0.7260536    0.7260536    0.7260536
##          -0.825512855 -0.874226881 -0.96572225 0.042118192 0.173328997
## estimate    4.0576335    4.0576335   4.0576335   4.0576335   4.0576335
## se          0.7260536    0.7260536   0.7260536   0.7260536   0.7260536
##          0.867471889 2.30436465 inode3122 inode3123 inode3151 inode3159
## estimate   4.0576335  4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se         0.7260536  0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 
## 
## Half life (another way of reporting alpha)
## -0.115762862 -0.218459259 -0.276269351 -0.324668291 -0.334277933 
##    308643937    308643937    308643937    308643937    308643937 
## -0.343935613 -0.347029762  -0.36429282  -0.36971411 -0.376347838 
##    308643937    308643937    308643937    308643937    308643937 
## -0.395173036 -0.399213836 -0.399284019  -0.40249729 -0.419749836 
##    308643937    308643937    308643937    308643937    308643937 
## -0.422992017 -0.449261397 -0.451042648 -0.454790159   -0.4580531 
##    308643937    308643937    308643937    308643937    308643937 
## -0.458694297 -0.461032003 -0.466734078 -0.478411682 -0.494906486 
##    308643937    308643937    308643937    308643937    308643937 
## -0.496224454 -0.507701406  -0.52278517 -0.527324428 -0.527913521 
##    308643937    308643937    308643937    308643937    308643937 
## -0.535408592 -0.539435104 -0.548287973 -0.555961591 -0.569277353 
##    308643937    308643937    308643937    308643937    308643937 
## -0.580540919 -0.581015956 -0.600904674 -0.651365854 -0.665162495 
##    308643937    308643937    308643937    308643937    308643937 
## -0.684832772  -0.69527236 -0.709372748 -0.731309262 -0.779848299 
##    308643937    308643937    308643937    308643937    308643937 
## -0.825512855 -0.874226881  -0.96572225  0.042118192  0.173328997 
##    308643937    308643937    308643937    308643937    308643937 
##  0.867471889   2.30436465    inode3122    inode3123    inode3151 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3159    inode3160    inode3162    inode3217    inode3218 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3219    inode3238    inode3239    inode3241    inode3242 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3246    inode3259    inode3264    inode3269    inode3272 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3274    inode3279    inode3280    inode3282    inode3284 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3288    inode3290    inode3297    inode3301    inode3315 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3316    inode3319    inode3326    inode3351    inode3490 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3495    inode3496    inode3501    inode3502    inode3509 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3513    inode3514    inode3525    inode3538    inode3542 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3572    inode3631    inode3714    inode3732    inode3769 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3970    inode4032    inode4086 
##    308643937    308643937    308643937 
## 
## Arrived at a reliable solution
OU1_KSPI$eigval
## [1] 2.6e+01 1.3e-06
OU1_KSPI$solution.se
##          -0.115762862 -0.218459259 -0.276269351 -0.324668291 -0.334277933
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.343935613 -0.347029762 -0.36429282 -0.36971411 -0.376347838
## alpha     882.7127566  882.7127566 882.7127566 882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103   0.1961103   0.1961103    0.1961103
##          -0.395173036 -0.399213836 -0.399284019 -0.40249729 -0.419749836
## alpha     882.7127566  882.7127566  882.7127566 882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103   0.1961103    0.1961103
##          -0.422992017 -0.449261397 -0.451042648 -0.454790159  -0.4580531
## alpha     882.7127566  882.7127566  882.7127566  882.7127566 882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103   0.1961103
##          -0.458694297 -0.461032003 -0.466734078 -0.478411682 -0.494906486
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.496224454 -0.507701406 -0.52278517 -0.527324428 -0.527913521
## alpha     882.7127566  882.7127566 882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103   0.1961103    0.1961103    0.1961103
##          -0.535408592 -0.539435104 -0.548287973 -0.555961591 -0.569277353
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.580540919 -0.581015956 -0.600904674 -0.651365854 -0.665162495
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.684832772 -0.69527236 -0.709372748 -0.731309262 -0.779848299
## alpha     882.7127566 882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103   0.1961103    0.1961103    0.1961103    0.1961103
##          -0.825512855 -0.874226881 -0.96572225 0.042118192 0.173328997
## alpha     882.7127566  882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq    0.1961103    0.1961103   0.1961103   0.1961103   0.1961103
##          0.867471889  2.30436465   inode3122   inode3123   inode3151
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3159   inode3160   inode3162   inode3217   inode3218
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3219   inode3238   inode3239   inode3241   inode3242
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3246   inode3259   inode3264   inode3269   inode3272
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3274   inode3279   inode3280   inode3282   inode3284
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3288   inode3290   inode3297   inode3301   inode3315
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3316   inode3319   inode3326   inode3351   inode3490
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3495   inode3496   inode3501   inode3502   inode3509
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3513   inode3514   inode3525   inode3538   inode3542
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3572   inode3631   inode3714   inode3732   inode3769
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3970   inode4032   inode4086
## alpha    882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103

OUM

OUM_KSPI<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OUM_KSPI
## 
## Fit
##       lnL       AIC     AICc       BIC model ntax
##  85.24088 -152.4818 -148.196 -134.9206   OUM   52
## 
## 
## Rates
##                   1          2          3          4          5          6
## alpha    5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
##                   7
## alpha    5.78373949
## sigma.sq 0.02552326
## 
## Optima
##                   1          2          3          4          5          6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se       0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
##                   7
## estimate 6.99998674
## se       0.01485411
## 
## 
## Half life (another way of reporting alpha)
##         1         2         3         4         5         6         7 
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 
## 
## Arrived at a reliable solution

AIC

aic<-setNames(c(BM1_KSPI$AICc,OU1_KSPI$AICc,OUM_KSPI$AICc),
              c("BM","OU1","OUM"))
aic
##        BM       OU1       OUM 
##  158.5073  160.7624 -148.1960
aic.w(aic)
##  BM OU1 OUM 
##   0   0   1

GF

dat<-read.csv("./data/Ouwie_data/GF_OUwie_ManyOptions_optima.csv")

BM

BM1_GF<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
BM1_GF
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 158.2624 158.5073 162.1649   BM1   52
## 
## Rates
##          -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## alpha              NA           NA           NA           NA          NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937  0.04805937
##          -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## alpha              NA           NA           NA          NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937  0.04805937   0.04805937
##          -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## alpha              NA           NA           NA           NA           NA
## sigma.sq   0.04805937   0.04805937   0.04805937   0.04805937   0.04805937
##          0.079914355 1.349473949  inode3122  inode3123  inode3151
## alpha             NA          NA         NA         NA         NA
## sigma.sq  0.04805937  0.04805937 0.04805937 0.04805937 0.04805937
##           inode3159  inode3160  inode3162  inode3217  inode3218  inode3219
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3238  inode3239  inode3241  inode3242  inode3246  inode3259
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3264  inode3269  inode3272  inode3274  inode3279  inode3280
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3282  inode3284  inode3288  inode3290  inode3297  inode3301
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3315  inode3316  inode3319  inode3326  inode3351  inode3490
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3495  inode3496  inode3501  inode3502  inode3509  inode3513
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3514  inode3525  inode3538  inode3542  inode3572  inode3631
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##           inode3714  inode3732  inode3769  inode3970  inode4032  inode4086
## alpha            NA         NA         NA         NA         NA         NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 
## Optima
##          -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## estimate    4.0576335            0            0            0            0
## se          0.7261147            0            0            0            0
##          -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## estimate            0            0            0            0           0
## se                  0            0            0            0           0
##          -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## estimate            0            0            0           0            0
## se                  0            0            0           0            0
##          -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## estimate            0            0            0            0            0
## se                  0            0            0            0            0
##          0.079914355 1.349473949 inode3122 inode3123 inode3151 inode3159
## estimate           0           0         0         0         0         0
## se                 0           0         0         0         0         0
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate         0         0         0         0         0         0
## se               0         0         0         0         0         0
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate         0         0         0         0         0
## se               0         0         0         0         0
## 
## Arrived at a reliable solution

OU1

OU1_GF<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OU1_GF
## 
## Fit
##        lnL      AIC     AICc      BIC model ntax
##  -77.13118 160.2624 160.7624 166.1161   OU1   52
## 
## Rates
##          -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.409662437 -0.419808798 -0.423308801 -0.425565648  -0.42583897
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.438880858 -0.448896787 -0.454790159  -0.45813357 -0.460589809
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##          -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##           0.079914355  1.349473949    inode3122    inode3123    inode3151
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3159    inode3160    inode3162    inode3217    inode3218
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3219    inode3238    inode3239    inode3241    inode3242
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3246    inode3259    inode3264    inode3269    inode3272
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3274    inode3279    inode3280    inode3282    inode3284
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3288    inode3290    inode3297    inode3301    inode3315
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3316    inode3319    inode3326    inode3351    inode3490
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3495    inode3496    inode3501    inode3502    inode3509
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3513    inode3514    inode3525    inode3538    inode3542
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3572    inode3631    inode3714    inode3732    inode3769
## alpha    2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
##             inode3970    inode4032    inode4086
## alpha    2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
## 
## 
## Optima
##          -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## estimate    4.0576335    4.0576335    4.0576335    4.0576335   4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536   0.7260536
##          -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## estimate    4.0576335    4.0576335    4.0576335   4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536   0.7260536    0.7260536
##          -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## estimate    4.0576335    4.0576335    4.0576335    4.0576335    4.0576335
## se          0.7260536    0.7260536    0.7260536    0.7260536    0.7260536
##          0.079914355 1.349473949 inode3122 inode3123 inode3151 inode3159
## estimate   4.0576335   4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se         0.7260536   0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##          inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se       0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 
## 
## Half life (another way of reporting alpha)
## -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123 
##    308643937    308643937    308643937    308643937    308643937 
## -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169 
##    308643937    308643937    308643937    308643937    308643937 
## -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302 
##    308643937    308643937    308643937    308643937    308643937 
## -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486 
##    308643937    308643937    308643937    308643937    308643937 
## -0.409662437 -0.419808798 -0.423308801 -0.425565648  -0.42583897 
##    308643937    308643937    308643937    308643937    308643937 
## -0.438880858 -0.448896787 -0.454790159  -0.45813357 -0.460589809 
##    308643937    308643937    308643937    308643937    308643937 
## -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314 
##    308643937    308643937    308643937    308643937    308643937 
## -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591 
##    308643937    308643937    308643937    308643937    308643937 
## -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762 
##    308643937    308643937    308643937    308643937    308643937 
## -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872 
##    308643937    308643937    308643937    308643937    308643937 
##  0.079914355  1.349473949    inode3122    inode3123    inode3151 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3159    inode3160    inode3162    inode3217    inode3218 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3219    inode3238    inode3239    inode3241    inode3242 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3246    inode3259    inode3264    inode3269    inode3272 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3274    inode3279    inode3280    inode3282    inode3284 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3288    inode3290    inode3297    inode3301    inode3315 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3316    inode3319    inode3326    inode3351    inode3490 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3495    inode3496    inode3501    inode3502    inode3509 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3513    inode3514    inode3525    inode3538    inode3542 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3572    inode3631    inode3714    inode3732    inode3769 
##    308643937    308643937    308643937    308643937    308643937 
##    inode3970    inode4032    inode4086 
##    308643937    308643937    308643937 
## 
## Arrived at a reliable solution
OU1_GF$eigval
## [1] 2.6e+01 1.3e-06
OU1_GF$solution.se
##          -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## alpha     882.7127566  882.7127566  882.7127566  882.7127566 882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103   0.1961103
##          -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## alpha     882.7127566  882.7127566  882.7127566 882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103   0.1961103    0.1961103
##          -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## alpha     882.7127566  882.7127566  882.7127566  882.7127566  882.7127566
## sigma.sq    0.1961103    0.1961103    0.1961103    0.1961103    0.1961103
##          0.079914355 1.349473949   inode3122   inode3123   inode3151
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3159   inode3160   inode3162   inode3217   inode3218
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3219   inode3238   inode3239   inode3241   inode3242
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3246   inode3259   inode3264   inode3269   inode3272
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3274   inode3279   inode3280   inode3282   inode3284
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3288   inode3290   inode3297   inode3301   inode3315
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3316   inode3319   inode3326   inode3351   inode3490
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3495   inode3496   inode3501   inode3502   inode3509
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3513   inode3514   inode3525   inode3538   inode3542
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3572   inode3631   inode3714   inode3732   inode3769
## alpha    882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103   0.1961103   0.1961103
##            inode3970   inode4032   inode4086
## alpha    882.7127566 882.7127566 882.7127566
## sigma.sq   0.1961103   0.1961103   0.1961103

OUM

OUM_GF<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing... 
## Finished. Begin thorough search... 
## Finished. Summarizing results.
OUM_GF
## 
## Fit
##       lnL       AIC     AICc       BIC model ntax
##  85.24088 -152.4818 -148.196 -134.9206   OUM   52
## 
## 
## Rates
##                   1          2          3          4          5          6
## alpha    5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
##                   7
## alpha    5.78373949
## sigma.sq 0.02552326
## 
## Optima
##                   1          2          3          4          5          6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se       0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
##                   7
## estimate 6.99998674
## se       0.01485411
## 
## 
## Half life (another way of reporting alpha)
##         1         2         3         4         5         6         7 
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 
## 
## Arrived at a reliable solution

AIC

aic<-setNames(c(BM1_GF$AICc,OU1_GF$AICc,OUM_GF$AICc),
              c("BM","OU1","OUM"))
aic
##        BM       OU1       OUM 
##  158.5073  160.7624 -148.1960
aic.w(aic)
##  BM OU1 OUM 
##   0   0   1
devtools::session_info()
## ─ Session info ──────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 3.5.2 (2018-12-20)
##  os       macOS Mojave 10.14.6        
##  system   x86_64, darwin15.6.0        
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       Asia/Tokyo                  
##  date     2019-10-17                  
## 
## ─ Packages ──────────────────────────────────────────────────────────────
##  package           * version   date       lib
##  animation           2.6       2018-12-11 [1]
##  ape               * 5.3       2019-03-17 [1]
##  assertthat          0.2.1     2019-03-21 [1]
##  backports           1.1.4     2019-04-10 [1]
##  BAMMtools         * 2.1.6     2017-02-03 [1]
##  bitops              1.0-6     2013-08-17 [1]
##  broom               0.5.2     2019-04-07 [1]
##  callr               3.2.0     2019-03-15 [1]
##  captioner         * 2.2.3     2015-07-16 [1]
##  caTools             1.17.1.2  2019-03-06 [1]
##  cellranger          1.1.0     2016-07-27 [1]
##  cli                 1.1.0     2019-03-19 [1]
##  clusterGeneration   1.3.4     2015-02-18 [1]
##  coda              * 0.19-2    2018-10-08 [1]
##  codetools           0.2-16    2018-12-24 [1]
##  colorspace          1.4-1     2019-03-18 [1]
##  combinat            0.0-8     2012-10-29 [1]
##  corHMM              1.22      2017-07-19 [1]
##  corpcor             1.6.9     2017-04-01 [1]
##  crayon              1.3.4     2017-09-16 [1]
##  desc                1.2.0     2018-05-01 [1]
##  deSolve             1.21      2018-05-09 [1]
##  devtools            2.0.2     2019-04-08 [1]
##  digest              0.6.19    2019-05-20 [1]
##  dplyr             * 0.8.1     2019-05-14 [1]
##  evaluate            0.14      2019-05-28 [1]
##  expm                0.999-4   2019-03-21 [1]
##  fastmatch           1.1-0     2017-01-28 [1]
##  forcats           * 0.4.0     2019-02-17 [1]
##  fs                  1.3.1     2019-05-06 [1]
##  gdata               2.18.0    2017-06-06 [1]
##  geiger            * 2.0.6.1   2019-01-16 [1]
##  generics            0.0.2     2018-11-29 [1]
##  GenSA               1.1.7     2018-01-17 [1]
##  ggplot2           * 3.1.1     2019-04-07 [1]
##  glue                1.3.1     2019-03-12 [1]
##  gmp                 0.5-13.5  2019-03-11 [1]
##  gplots              3.0.1.1   2019-01-27 [1]
##  gtable              0.3.0     2019-03-25 [1]
##  gtools              3.8.1     2018-06-26 [1]
##  haven               2.1.0     2019-02-19 [1]
##  hms                 0.4.2     2018-03-10 [1]
##  htmltools           0.3.6     2017-04-28 [1]
##  httr                1.4.0     2018-12-11 [1]
##  igraph              1.2.4.1   2019-04-22 [1]
##  jsonlite            1.6       2018-12-07 [1]
##  kableExtra        * 1.1.0     2019-03-16 [1]
##  KernSmooth          2.23-15   2015-06-29 [1]
##  knitr               1.23      2019-05-18 [1]
##  lattice           * 0.20-38   2018-11-04 [1]
##  lazyeval            0.2.2     2019-03-15 [1]
##  lubridate           1.7.4     2018-04-11 [1]
##  magrittr            1.5       2014-11-22 [1]
##  maps              * 3.3.0     2018-04-03 [1]
##  MASS                7.3-51.4  2019-03-31 [1]
##  Matrix              1.2-17    2019-03-22 [1]
##  memoise             1.1.0     2017-04-21 [1]
##  mnormt              1.5-5     2016-10-15 [1]
##  modelr              0.1.4     2019-02-18 [1]
##  munsell             0.5.0     2018-06-12 [1]
##  mvtnorm             1.0-10    2019-03-05 [1]
##  nlme                3.1-140   2019-05-12 [1]
##  nloptr            * 1.2.1     2018-10-03 [1]
##  nnet                7.3-12    2016-02-02 [1]
##  numDeriv            2016.8-1  2016-08-27 [1]
##  OUwie             * 1.53      2019-06-11 [1]
##  paleotree           3.3.0     2019-06-04 [1]
##  phangorn            2.5.3     2019-03-23 [1]
##  phytools          * 0.6-60    2018-09-28 [1]
##  pillar              1.4.1     2019-05-28 [1]
##  pkgbuild            1.0.3     2019-03-20 [1]
##  pkgconfig           2.0.2     2018-08-16 [1]
##  pkgload             1.0.2     2018-10-29 [1]
##  plotrix             3.7-5     2019-04-07 [1]
##  plyr                1.8.4     2016-06-08 [1]
##  png                 0.1-7     2013-12-03 [1]
##  prettyunits         1.0.2     2015-07-13 [1]
##  processx            3.3.1     2019-05-08 [1]
##  ps                  1.3.0     2018-12-21 [1]
##  purrr             * 0.3.2     2019-03-15 [1]
##  quadprog            1.5-7     2019-05-06 [1]
##  R6                  2.4.0     2019-02-14 [1]
##  Rcpp                1.0.1     2019-03-17 [1]
##  RCurl               1.95-4.12 2019-03-04 [1]
##  readr             * 1.3.1     2018-12-21 [1]
##  readxl              1.3.1     2019-03-13 [1]
##  remotes             2.0.4     2019-04-10 [1]
##  reshape2          * 1.4.3     2017-12-11 [1]
##  rlang               0.3.4     2019-04-07 [1]
##  rmarkdown           1.13      2019-05-22 [1]
##  Rmpfr               0.7-2     2019-01-22 [1]
##  rprojroot           1.3-2     2018-01-03 [1]
##  rstudioapi          0.10      2019-03-19 [1]
##  rvest               0.3.4     2019-05-15 [1]
##  scales              1.0.0     2018-08-09 [1]
##  scatterplot3d       0.3-41    2018-03-14 [1]
##  sessioninfo         1.1.1     2018-11-05 [1]
##  spptest           * 0.4       2019-07-10 [1]
##  stringi             1.4.3     2019-03-12 [1]
##  stringr           * 1.4.0     2019-02-10 [1]
##  subplex             1.5-4     2018-04-05 [1]
##  testthat            2.1.1     2019-04-23 [1]
##  tibble            * 2.1.1     2019-03-16 [1]
##  tidyr             * 0.8.3     2019-03-01 [1]
##  tidyselect          0.2.5     2018-10-11 [1]
##  tidyverse         * 1.2.1     2017-11-14 [1]
##  usethis             1.5.0     2019-04-07 [1]
##  viridisLite         0.3.0     2018-02-01 [1]
##  webshot             0.5.1     2018-09-28 [1]
##  withr               2.1.2     2018-03-15 [1]
##  xfun                0.7       2019-05-14 [1]
##  xml2                1.2.0     2018-01-24 [1]
##  yaml                2.2.0     2018-07-25 [1]
##  source                         
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## [1] /Library/Frameworks/R.framework/Versions/3.5/Resources/library